antarna: antaRNA.py annotate

annotate antaRNA.py @ 18:a9a0fb585968 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty

author	rnateam
date	Wed, 13 May 2015 10:58:00 -0400
parents	2f68c8d1c080
children

rev	line source
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1 import numpy
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	2 import sys
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	3 import random
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	4 import subprocess
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	5 import re
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	6 import decimal
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	7 import math
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	8 import os
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	9 import shutil
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	10 import time
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	11 import types
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	12 import argparse
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	13 #from argparse import RawTextHelpFormatter
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	14
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	15 #############################
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	16 # FUNCTIONS
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	17
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	18 def print2file(f, i, m):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	19 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	20 print content i to file f in mode m
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	21 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	22 line = str(i)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	23 if m == "a":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	24 call = "echo \"" + line + "\" >> " + f
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	25 elif m == "w":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	26 call = "echo \"" + line + "\" > " + f
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	27 os.system(call)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	28
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	29 # checking and correcting the alphabet of the constraint sequence
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	30 def checkSequenceConstraint(SC):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	31 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	32 Checks the Sequence constraint for illegal nucleotide characters
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	33 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	34 out = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	35 for c in SC:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	36 c = c.upper()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	37 if c not in "ACGURYSWKMBDHVN":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	38 # and c!= "R" and c != "Y" and c != "S" and c != "W" and c != "K" and c != "M" and c != "B" and c != "D" and c != "H" and c != "V":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	39 if c == "T":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	40 c = "U"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	41 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	42 print "\tIllegal Character in the constraint sequence!"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	43 print "\tPlease use the IUPAC nomenclature for defining nucleotides in the constraint sequence!"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	44 print "\tA Adenine"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	45 print "\tC Cytosine"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	46 print "\tG Guanine"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	47 print "\tT/U Thymine/Uracil"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	48 print "\tR A or G"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	49 print "\tY C or T/U"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	50 print "\tS G or C"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	51 print "\tW A or T/U"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	52 print "\tK G or T/U"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	53 print "\tM A or C"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	54 print "\tB C or G or T/U"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	55 print "\tD A or G or T/U"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	56 print "\tH A or C or T/U"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	57 print "\tV A or C or G"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	58 print "\tN any base"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	59 exit(0)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	60 out += c
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	61 return (1, out)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	62
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	63
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	64 def transform(seq):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	65 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	66 Transforms "U" to "T" for the processing is done on DNA alphabet
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	67 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	68 S = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	69 for s in seq:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	70 if s == "T":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	71 S += "U"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	72 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	73 S += s
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	74 return S
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	75
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	76
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	77 def checkSimilarLength(s, SC):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	78 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	79 Compares sequence and structure constraint length
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	80 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	81 if len(s) == len(SC):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	82 return 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	83 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	84 return 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	85
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	86
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	87 def isStructure(s):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	88 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	89 Checks if the structure constraint only contains "(", ")", and "." and legal fuzzy structure constraint characters.
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	90 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	91 returnvalue = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	92 for a in range(0,len(s)):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	93 if s[a] not in ".()[]{}<>":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	94 if s[a] not in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	95 returnvalue = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	96 return returnvalue
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	97
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	98
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	99 def isBalanced(s):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	100 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	101 Check if the structure s is of a balanced nature
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	102 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	103
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	104 balance = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	105 for bracket in ["()", "[]", "{}", "<>"]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	106 counter = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	107 for a in xrange(len(s)):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	108 if s[a] in bracket[0]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	109 counter += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	110 elif s[a] in bracket[1]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	111 counter -= 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	112 if counter != 0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	113 balance = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	114 return balance
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	115
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	116
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	117
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	118 def fulfillsHairpinRule(s):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	119 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	120 CHECKING FOR THE 3 nt LOOP INTERSPACE
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	121 for all kind of basepairs, even wihtin the pdeudoknots
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	122 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	123
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	124 fulfillsRules = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	125 for bracket in ["()", "[]", "{}", "<>"]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	126 last_opening_char = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	127 check = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	128 for a in xrange(len(s)):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	129 if s[a] == bracket[0]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	130 last_opening_char = a
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	131 check = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	132 elif s[a] == bracket[1] and check == 1:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	133 check = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	134 if a - last_opening_char < 4:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	135 return 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	136 return 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	137
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	138
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	139 def isValidStructure(s):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	140 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	141 Checks, if the structure s is a valid structure
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	142 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	143
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	144 Structure = isStructure(s)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	145 Balanced = isBalanced(s)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	146 HairpinRule = fulfillsHairpinRule(s)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	147
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	148 if Structure == 1 and Balanced == 1 and HairpinRule == 1:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	149 return 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	150 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	151 print Structure, Balanced, HairpinRule
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	152 return 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	153
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	154 def loadIUPACcompatibilities(IUPAC, useGU):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	155 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	156 Generating a hash containing all compatibilities of all IUPAC RNA NUCLEOTIDES
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	157 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	158 compatible = {}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	159 for nuc1 in IUPAC: # ITERATING OVER THE DIFFERENT GROUPS OF IUPAC CODE
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	160 sn1 = list(IUPAC[nuc1])
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	161 for nuc2 in IUPAC: # ITERATING OVER THE DIFFERENT GROUPS OF IUPAC CODE
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	162 sn2 = list(IUPAC[nuc2])
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	163 compatib = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	164 for c1 in sn1: # ITERATING OVER THE SINGLE NUCLEOTIDES WITHIN THE RESPECTIVE IUPAC CODE:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	165 for c2 in sn2: # ITERATING OVER THE SINGLE NUCLEOTIDES WITHIN THE RESPECTIVE IUPAC CODE:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	166 # CHECKING THEIR COMPATIBILITY
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	167 if useGU == True:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	168 if (c1 == "A" and c2 == "U") or (c1 == "U" and c2 == "A") or (c1 == "C" and c2 == "G") or (c1 == "G" and c2 == "C") or (c1 == "G" and c2 == "U") or (c1 == "U" and c2 == "G"):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	169 compatib = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	170 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	171 if (c1 == "A" and c2 == "U") or (c1 == "U" and c2 == "A") or (c1 == "C" and c2 == "G") or (c1 == "G" and c2 == "C"):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	172 compatib = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	173 compatible[nuc1 + "_" + nuc2] = compatib # SAVING THE RESPECTIVE GROUP COMPATIBILITY, REVERSE SAVING IS NOT REQUIRED, SINCE ITERATING OVER ALL AGAINST ALL
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	174 return compatible
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	175
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	176 def isCompatibleToSet(c1, c2, IUPAC_compatibles):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	177 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	178 Checks compatibility of c1 wihtin c2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	179 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	180 compatible = True
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	181 for setmember in c2:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	182 #print setmember
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	183 if isCompatible(c1, setmember, IUPAC_compatibles) == False:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	184 return False
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	185 return compatible
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	186
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	187
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	188 def isCompatible(c1, c2, IUPAC_compatibles):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	189 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	190 Checks compatibility between character c1 and c2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	191 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	192 if IUPAC_compatibles[c1 + "_" + c2] == 1:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	193 return True
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	194 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	195 return False
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	196
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	197
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	198 def isStructureCompatible(lp1, lp2 ,bp):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	199 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	200 Checks, if the region within lp1 and lp2 is structurally balanced
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	201 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	202 x = lp1 + 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	203 while (x < lp2):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	204 if (bp[x] <= lp1 or bp[x] > lp2):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	205 return False
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	206 if x == bp[x]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	207 x += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	208 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	209 x = bp[x] + 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	210 return x == lp2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	211
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	212
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	213 def checkConstaintCompatibility(basepairstack, sequenceconstraint, IUPAC_compatibles):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	214 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	215 Checks if the constraints are compatible to each other
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	216 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	217 returnstring = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	218 compatible = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	219 for id1 in basepairstack: # key = (constraint , (pos, constraint)))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	220 constr1 = basepairstack[id1][0]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	221 id2 = basepairstack[id1][1][0]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	222 constr2 = basepairstack[id1][1][1]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	223
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	224 if id1 != id2 and not isCompatible(constr1, constr2, IUPAC_compatibles):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	225
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	226 compatible = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	227 returnstring += "nucleotide constraint " + str(constr1) + " at position " + str(id1) + " is not compatible with nucleotide constraint " + str(constr2) + " at position " + str(id2) + "\n"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	228 #if not isCompatible(basepairstack[basepair][0], basepairstack[basepair][1][1]):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	229
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	230 #compatible = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	231 #else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	232 #returnstring += "nucleotide constraint " + str(basepairstack[basepair][0]) + " at position " + str(basepair) + " is compatible with nucleotide constraint " + str(basepairstack[basepair][1][1]) + " at position " + str(basepairstack[basepair][1][0]) + "\n"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	233 return (compatible, returnstring)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	234
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	235
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	236 def getLP(BPSTACK):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	237 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	238 Retreives valid lonley base pairs from a base pair stack
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	239 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	240 #20 ('N', (>BLOCK<, 'N'))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	241
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	242 # geting single base pairs
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	243 stack = {}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	244 LP = {}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	245 if type(BPSTACK[random.choice(BPSTACK.keys())]) == types.TupleType:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	246 for i in BPSTACK.keys():
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	247 #if str(BPSTACK[i][1][0]) not in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	248 stack[i] = int(BPSTACK[i][1][0])
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	249 #print i , BPSTACK[i][1][0]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	250 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	251 for i in BPSTACK.keys():
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	252 #if str(BPSTACK[i]) not in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	253 stack[i] = BPSTACK[i]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	254
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	255 # removing redundant base pair indices
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	256 for i in stack.keys():
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	257 if i >= stack[i]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	258 del stack[i]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	259
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	260 # actual checking for single lonley base pairs
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	261 for i in stack.keys():
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	262 if not (i-1 in stack and stack[i-1] == stack[i] + 1) and not (i+1 in stack and stack[i+1] == stack[i] - 1):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	263 LP[i] = stack[i]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	264
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	265 ##actual removal of 2er lonley base pairs
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	266 for i in stack.keys():
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	267 if not (i-1 in stack and stack[i-1] == stack[i] + 1) and (i+1 in stack and stack[i+1] == stack[i] - 1) and not (i+2 in stack and stack[i+2] == stack[i] - 2):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	268 LP[i] = stack[i]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	269 LP[i+1] = stack[i+1]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	270
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	271
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	272 #if type(BPSTACK[random.choice(BPSTACK.keys())]) == types.TupleType:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	273 #for i in BPSTACK.keys():
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	274
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	275 ##if str(BPSTACK[i][1][0]) not in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	276 #stack[i] = int(BPSTACK[i][1][0])
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	277 ##print i , BPSTACK[i][1][0]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	278 #else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	279 #for i in BPSTACK.keys():
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	280 ##if str(BPSTACK[i]) not in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	281 #stack[i] = BPSTACK[i]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	282
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	283 #for i in stack.keys():
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	284 #if i >= stack[i]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	285 #del stack[i]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	286
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	287
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	288
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	289 return LP
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	290
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	291
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	292 def getBPStack(s, seq):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	293 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	294 Returns a dictionary of the corresponding basepairs of the structure s and the sequence constraint seq.
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	295 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	296 tmp_stack = {"()":[], "{}":[], "[]":[], "<>":[]}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	297 bpstack = {}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	298 for i in xrange(len(s)):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	299
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	300 # REGULAR SECONDARY STRUCTURE DETECTION
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	301 if s[i] in "(){}[]<>":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	302
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	303 no = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	304 ### opening
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	305 if s[i] in "([{<":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	306 if s[i] == "(":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	307 tmp_stack["()"].append((i, seq[i]))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	308 elif s[i] == "[":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	309 tmp_stack["[]"].append((i, seq[i]))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	310 elif s[i] == "{":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	311 tmp_stack["{}"].append((i, seq[i]))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	312 elif s[i] == "<":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	313 tmp_stack["<>"].append((i, seq[i]))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	314
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	315 #closing
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	316 elif s[i] in ")]}>":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	317 if s[i] == ")":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	318 no, constr = tmp_stack["()"].pop()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	319 elif s[i] == "]":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	320 no, constr = tmp_stack["[]"].pop()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	321 elif s[i] == "}":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	322 no, constr = tmp_stack["{}"].pop()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	323 elif s[i] == ">":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	324 no, constr = tmp_stack["<>"].pop()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	325 bpstack[no] = (constr, (i, seq[i]))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	326 bpstack[i] = (seq[i] ,(no, constr))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	327
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	328 elif s[i] == ".":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	329 bpstack[i] = (seq[i], (i, seq[i]))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	330 elif s[i] in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	331 bpstack[i] = (seq[i], (i, seq[i]))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	332
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	333 return (bpstack, getLP(bpstack))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	334
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	335
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	336 def getbpStack(s):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	337 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	338 Returns a dictionary of the corresponding basepairs of the structure s and the sequence constraint seq.
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	339 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	340 tmp_stack = {"()":[], "{}":[], "[]":[], "<>":[]}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	341 bpstack = {}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	342
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	343 for i in xrange(len(s)):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	344 if s[i] in "(){}[]<>":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	345
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	346 no = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	347 ### opening
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	348 if s[i] in "([{<":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	349 if s[i] == "(":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	350 tmp_stack["()"].append(i)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	351 elif s[i] == "[":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	352 tmp_stack["[]"].append(i)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	353 elif s[i] == "{":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	354 tmp_stack["{}"].append(i)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	355 elif s[i] == "<":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	356 tmp_stack["<>"].append(i)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	357
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	358 #closing
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	359 elif s[i] in ")]}>":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	360 if s[i] == ")":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	361 no = tmp_stack["()"].pop()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	362 elif s[i] == "]":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	363 no = tmp_stack["[]"].pop()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	364 elif s[i] == "}":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	365 no = tmp_stack["{}"].pop()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	366 elif s[i] == ">":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	367 no = tmp_stack["<>"].pop()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	368 bpstack[no] = i # save basepair in the format {opening base id (opening seq constr,(closing base id, closing seq constr))}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	369 bpstack[i] = no # save basepair in the format {closing base id (closing seq constr,(opening base id, opening seq constr))}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	370
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	371 elif s[i] == ".": # no structural constaint given: produce entry, which references itself as a base pair partner....
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	372 bpstack[i] = i
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	373
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	374 elif s[i] in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	375 bpstack[i] = i
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	376
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	377 #elif s[i] in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	378 ## per position, assigned to a certain block, the target nucleotide, with whcih it should interact is marked with the specific
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	379 ## block character
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	380 #bpstack[i] = s[i]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	381
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	382 return (bpstack, getLP(bpstack))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	383
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	384 def maprange( a, b, s):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	385 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	386 Mapping function
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	387 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	388 (a1, a2), (b1, b2) = a, b
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	389 return b1 + ((s - a1) * (b2 - b1) / (a2 - a1))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	390
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	391
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	392 def applyGCcontributionPathAdjustment(pathlength, tmpGC, nt):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	393 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	394 GC path length contribution calculation.
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	395 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	396 GCadjustment = 1.5
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	397 minimum = 0.5
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	398 upper = GCadjustment
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	399 lower = minimum
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	400
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	401 if nt == "A" or nt == "U":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	402 pathlength = pathlength * maprange( (0, 1) , (lower, upper), tmpGC)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	403
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	404 if nt == "G" or nt == "C":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	405 #pathlength = pathlength * (float(1-tmpGC))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	406 pathlength = pathlength * maprange( (1, 0) , (lower, upper), tmpGC)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	407 return pathlength
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	408
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	409 def getConstraint(TE, BPstack, IUPAC, IUPAC_compatibles, IUPAC_reverseComplements):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	410 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	411 Dependend on the situation in the constraint an the respective path section, setting wether a specific constraint can be given or not (for that path section)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	412 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	413 # TE :: transition element / path section under dispute
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	414 # id1 :: id of the position of the caharacter to which the transition is leading to
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	415 # id2 :: id of the position of the character, which is listed in the BPinformation, it can be id1 as well, when no bp is present
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	416 # val :: BPstack information of the specific position
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	417 # constr1 :: constraining character of pos id1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	418 # constr2 :: constraining character of pos id2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	419
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	420 id1 = int(TE.split(".")[0])
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	421 val = BPstack[id1] # check out the value of the destination character in the basepair/constraint stack
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	422 constr1 = val[0] # getting the constraint character of position id1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	423 id2 = int(val[1][0]) # getting position id2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	424 constr2 = val[1][1] # getting the sequence constraint for position id2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	425 targetNucleotide = TE.split(".")[1][-1:] # where the edge is leading to
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	426
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	427 c1 = set(IUPAC[constr1]) # getting all explicit symbols of c1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	428 c2 = set(IUPAC_reverseComplements[constr2]) # getting the reverse complement explicit symbols of c2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	429
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	430 if targetNucleotide in c1:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	431 if id1 == id2:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	432 return 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	433 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	434 if targetNucleotide in c2:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	435 return 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	436 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	437 return 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	438 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	439 return 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	440
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	441 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	442 def getConstraint(TE, BPstack):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	443 # TE :: transition element / path section
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	444 # id1 :: id of the position of the caharacter to which the transition is leading to
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	445 # id2 :: id of the position of the character, which is listed in the BPinformation, it can be id1 as well, when no bp is present
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	446 # val :: BPstack information of the specific position
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	447 # constr1 :: constraining character of pos id1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	448 # constr2 :: constraining character of pos id2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	449
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	450 ### BPstack [id1] = (constr1, (id2, constr2))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	451
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	452 id1 = TE.split(".")[0]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	453 #print id1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	454 #id1 = TE.find(TE.strip("_")) # strip the path section and getting the position of the section
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	455 #if len(TE.strip("_")) == 2: # check if the path section is from an internal and not an initial transition
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	456 #id1 += 1 # increase position id1 by 1, since the last character of the section is the destination character
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	457 val = BPstack[int(id1)] # check out the value of the destination character in the basepair/constraint stack
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	458 constr1 = val[0] # getting the constraint character of position id1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	459 id2 = val[1][0] # getting position id2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	460 constr2 = val[1][1] # getting the sequence constraint for position id2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	461 #print TE, id1, constr1, id2, constr2,
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	462
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	463 #TE.split(".")[1][-1:]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	464 if id1 == id2: # both ids were the same with either character, sequential or no sequential constraint -> no basepair constraint
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	465 if constr1 == TE.split(".")[1][-1:] and constr2 == TE.split(".")[1][-1:]: # case if the single base constraints on position id1 == id2 are the same as the destination character on id1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	466 #print 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	467 return 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	468 elif constr1 == constr2 == "N": # case if the single base constraints on position id1 == id2 has no constraint
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	469 #print 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	470 return 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	471 else: # single base sequence constraints differ
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	472 #print 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	473 return 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	474
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	475 elif id1 != id2: # showing differentq ids, indicating a bp, (basepair structural constraint)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	476 if constr1 == "N" and constr2 == "N": # no sequence constraint
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	477 #print 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	478 return 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	479 if constr1 == "N" and constr2 != "N": # c1 has no constraint, c2 has character constraint (sequence constraint of closing bases)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	480 if TE.split(".")[1][-1:] == complementBase(constr2): # the current path section destination base is equal to the complement base of the mentioned sequence constraint in constr2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	481 #print 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	482 return 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	483 else: # case if the current path section destination base is not equeal to the mentioned complement sequence constraint in constr2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	484 #print 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	485 return 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	486 if constr1 != "N" and constr2 == "N": # c1 has character constraint, c2 has no character constraint (sequence constraint in the opening base)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	487 if TE.split(".")[1][-1:] == constr1: # the current path section destination base is as constrained with constr1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	488 #print 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	489 return 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	490 else: # the current path section destination base is not as constrained in constr1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	491 #print 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	492 return 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	493 if constr1 != "N" and constr2 != "N": # both positions have sequential constraint
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	494 if TE.split(".")[1][-1:] == constr1:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	495 #print 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	496 return 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	497 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	498 #print 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	499 return 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	500 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	501
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	502 def applyTerrainModification(terrain, s, tmpGC, SC, BPstack, IUPAC, IUPAC_compatibles, IUPAC_reverseComplements):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	503 #nucleotides = {'A': 0, 'C': 1,'G': 2,'T': 3}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	504
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	505 dels = []
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	506 for terrainelement in sorted(terrain):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	507 pheromone, pathlength = terrain[terrainelement]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	508 pheromone = getConstraint(terrainelement, BPstack, IUPAC, IUPAC_compatibles, IUPAC_reverseComplements)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	509 pathlength = getConstraint(terrainelement, BPstack, IUPAC, IUPAC_compatibles, IUPAC_reverseComplements)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	510 pathlength = applyGCcontributionPathAdjustment(pathlength, tmpGC,terrainelement.split(".")[1][-1:])
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	511 if pheromone * pathlength == 0: dels.append(terrainelement)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	512 terrain[terrainelement] = (pheromone, pathlength,[])
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	513 further_dels = {}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	514 for terrainelement in sorted(dels):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	515 pos, nucs = terrainelement.split(".")
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	516 if int(pos) < len(s)-1:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	517 to_nt = nucs[-1:]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	518 successor_pos = int(pos) + 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	519 for i in ["A", "C", "G", "U"]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	520 del_element = str(successor_pos) + "." + to_nt + i
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	521 further_dels[del_element] = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	522 further_dels[terrainelement] = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	523 # deleting the inbound and outbound edges, which are forbidden
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	524 for terrainelement in further_dels:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	525 del terrain[terrainelement]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	526 # allocate the appropriate children of edges
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	527 for terrainelement in terrain:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	528 pheromone, pathlength, children = terrain[terrainelement]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	529 pos, nucs = terrainelement.split(".")
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	530 if int(pos) < len(s):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	531 to_nt = nucs[-1:]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	532 successor_pos = int(pos) + 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	533 for i in ["A", "C", "G", "U"]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	534 if str(successor_pos) + "." + to_nt + i in terrain:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	535 children.append(str(successor_pos) + "." + to_nt + i)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	536 terrain[terrainelement] = (pheromone, pathlength,children)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	537 starts = []
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	538 for i in ["A", "C", "G", "U"]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	539 if str(0) + "." + i in terrain:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	540 starts.append(str(0) + "." + i)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	541 terrain["00.XY"] = (1, 1, starts)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	542 return (terrain, BPstack)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	543
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	544
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	545 def initTerrain(s): # THE CLASSIC
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	546 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	547 Initialization of the terrain with graph like terrain... vertices are modeled implicitly
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	548 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	549 nt = ["A","C","G","U"]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	550 nt2 = ["AA","AC","AG","AU","CA","CC","CG","CU","GA","GC","GG","GU","UA","UC","UG","UU"] # Allowed dinucleotides
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	551 e = {}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	552 pathlength = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	553 pheromone = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	554 for p in xrange(len(s)):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	555 if p == 0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	556 for i in nt:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	557 e["%s.%s"%(p,i)] = (pheromone, pathlength)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	558 elif p > 0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	559 for n in nt2:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	560 e["%s.%s"%(p,n)] = (pheromone, pathlength)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	561 return e
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	562
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	563
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	564
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	565 def complementBase(c):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	566 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	567 Returns the complement RNA character of c (without GU base pairs)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	568 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	569 retChar = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	570 if c == "A" :
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	571 retChar = "U"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	572 elif c == "U":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	573 retChar = "A"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	574 elif c == "C":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	575 retChar = "G"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	576 elif c == "G":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	577 retChar = "C"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	578 return retChar
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	579
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	580 def printTerrain(terrain):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	581 #print sorted(terrain.keys())
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	582 tmp_i = "0"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	583 tmp_c = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	584 terrain = terrain[0]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	585
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	586 for a, i in enumerate(sorted(terrain.keys())):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	587 #print a
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	588 if i.split(".")[0] != tmp_i:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	589 print "\nElements:", tmp_c,"\n#########################\n", i, terrain[i]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	590
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	591 tmp_c = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	592 tmp_i = i.split(".")[0]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	593 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	594 print i, terrain[i]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	595 tmp_c += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	596
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	597 print "\nElements:", tmp_c
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	598 print "#########################"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	599 print len(terrain)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	600
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	601 def pickStep(tmp_steps, summe):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	602 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	603 Selects a step within the terrain
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	604 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	605 if len(tmp_steps) == 1:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	606 return tmp_steps[0][1] # returning the nucleotide of the only present step
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	607 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	608 rand = random.random() # draw random number
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	609 mainval = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	610 for choice in xrange(len(tmp_steps)):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	611 val, label = tmp_steps[choice]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	612 mainval += val/float(summe)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	613 if mainval > rand: # as soon, as the mainval gets larger than the random value the assignment is done
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	614 return label
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	615
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	616 def getPath(s, tmp_terrain, tmp_BPstack, alpha, beta, IUPAC, IUPAC_reverseComplements):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	617 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	618 Performs a walk through the terrain and assembles a sequence, while respecting the structure constraint and IUPAC base complementarity
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	619 of the base pairs GU, GC and AT
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	620 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	621 nt = ["A","C","G","U"]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	622 prev_edge = "00.XY"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	623 sequence = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	624 while len(sequence) < len(s):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	625 coming_from = sequence[-1:]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	626 summe = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	627 steps = []
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	628 i = len(sequence)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	629 allowed_nt = "ACGU"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	630 # base pair closing case check, with subsequent delivery of a reduced allowed nt set
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	631
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	632 if i > tmp_BPstack[i][1][0]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	633 jump = tmp_BPstack[i][1][0]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	634 nuc_at_jump = sequence[jump]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	635 allowed_nt = IUPAC_reverseComplements[nuc_at_jump]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	636
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	637 #allowed_nt = complementBase(nuc_at_jump)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	638
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	639 # Checking for every possible nt if it is suitable for the selection procedure
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	640 for edge in tmp_terrain[prev_edge][-1]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	641
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	642 if edge[-1:] in allowed_nt:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	643 pheromone, PL , children = tmp_terrain[edge]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	644 #if PL > 0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	645 value = ((float(pheromone * alpha)) + ((1/float(PL)) * beta))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	646 summe += value
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	647 steps.append((value, edge))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	648 prev_edge = pickStep(steps, summe)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	649 sequence += prev_edge[-1:]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	650
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	651 return sequence
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	652
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	653
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	654 ###
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	655 # STRUCTURE PREDICTORS
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	656 ###
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	657 def getPKStructure(sequence, temperature, mode = "A"):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	658 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	659 Initialization pKiss mfe pseudoknot prediction
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	660 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	661 p2p = "pKiss"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	662 #p2p = "/usr/local/pkiss/2014-03-17/bin/pKiss_mfe"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	663 strategy = "--strategy "
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	664 t = "--temperature " + str(temperature)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	665
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	666 if mode == "A": strategy += "A"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	667 elif mode == "B": strategy += "B"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	668 elif mode == "C": strategy += "C"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	669 elif mode == "D": strategy += "D"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	670 elif mode == "P": strategy += "P"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	671
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	672 p = subprocess.Popen( ([p2p, "--mode mfe", strategy, t]),
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	673 #shell = True,
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	674 stdin = subprocess.PIPE,
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	675 stdout = subprocess.PIPE,
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	676 stderr = subprocess.PIPE,
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	677 close_fds = True)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	678 #print p.stderr.readline()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	679
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	680 p.stdin.write(sequence+'\n')
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	681 pks = p.communicate()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	682 structure = "".join(pks[0].split("\n")[2].split(" ")[-1:])
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	683 return structure
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	684
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	685 def init_RNAfold(version, temperature, paramFile = ""):
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	686 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	687 Initialization RNAfold listener
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	688 """
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	689 p2p = ""
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	690 t = "-T " + str(temperature)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	691 P = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	692 if paramFile != "":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	693 P = "-P " + paramFile
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	694 if version == 185:
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	695 p2p = "/home/rk/Software/ViennaRNA/ViennaRNA-1.8.5/Progs/RNAfold"
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	696 p = subprocess.Popen( ([p2p, '--noPS', '-d 2', t, P]),
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	697 shell = True,
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	698 stdin = subprocess.PIPE,
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	699 stdout = subprocess.PIPE,
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	700 stderr = subprocess.PIPE,
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	701 close_fds = True)
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	702 return p
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	703 elif version == 213:
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	704 p2p = "RNAfold"
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	705 p = subprocess.Popen( ([p2p, '--noPS', '-d 2', t, P]),
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	706 #shell = True,
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	707 stdin = subprocess.PIPE,
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	708 stdout = subprocess.PIPE,
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	709 stderr = subprocess.PIPE,
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	710 close_fds = True)
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	711 return p
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	712 else:
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	713 exit(0)
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	714
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	715 def consult_RNAfold(seq, p):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	716 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	717 Consults RNAfold listener
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	718 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	719 p.stdin.write(seq+'\n')
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	720 out = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	721 for i in xrange(2):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	722 out += p.stdout.readline()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	723 return out
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	724
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	725
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	726 def getRNAfoldStructure(struct2, process1):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	727 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	728 Retrieves folded structure of a RNAfold call
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	729 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	730
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	731 RNAfold_pattern = re.compile('.+\n([.()]+)\s.+')
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	732 #RNAdist_pattern = re.compile('.*\s([\d]+)')
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	733 RNAfold_match = RNAfold_pattern.match(consult_RNAfold(struct2, process1))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	734 current_structure = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	735 #if RNAfold_match:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	736 return RNAfold_match.group(1)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	737
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	738
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	739 def init_RNAdistance():
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	740 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	741 Initialization of RNAdistance listener
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	742 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	743 #p2p = "/home/rk/Software/ViennaRNA/ViennaRNA-1.8.5/Progs/RNAdistance"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	744 p2p = "RNAdistance"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	745 p = subprocess.Popen( ([p2p]),
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	746 #shell = True,
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	747 stdin = subprocess.PIPE,
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	748 stdout = subprocess.PIPE,
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	749 stderr = subprocess.PIPE,
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	750 close_fds = True)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	751 return p
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	752
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	753
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	754 def consult_RNAdistance(s1, s2, p):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	755 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	756 Consulting the RNAdistance listener
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	757 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	758 p.stdin.write(s1+'\n')
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	759 p.stdin.write(s2+'\n')
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	760 out = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	761 out_tmp = p.stdout.readline().strip()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	762 if out_tmp != "":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	763 out += out_tmp
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	764 return out
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	765
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	766 def getInducingSequencePositions(Cseq, degreeOfSequenceInducement):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	767 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	768 Delimiting the degree of structure inducement by the supplied sequence constraint.
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	769 0 : no sequence induced structure constraint
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	770 1 : "ACGT" induce structure (explicit nucleotide structure inducement level)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	771 2 : "MWKSYR" and "ACGT" (explicit and double instances)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	772 3 : "BDHV" , "MWKSYR" and "ACGT" (explicit, double, and triple instances)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	773 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	774 setOfNucleotides = "" # resembling the "0"-case
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	775 if degreeOfSequenceInducement == 1:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	776 setOfNucleotides = "ACGU"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	777 elif degreeOfSequenceInducement == 2:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	778 setOfNucleotides = "ACGUMWKSYR"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	779 elif degreeOfSequenceInducement == 3:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	780 setOfNucleotides = "ACGUMWKSYRBDHV"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	781 #elif degreeOfSequenceInducement == 4:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	782 #setOfNucleotides = "ACGTMWKSYRBDHVN"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	783
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	784 tmpSeq = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	785 listset = setOfNucleotides
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	786 for pos in Cseq:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	787 if pos not in listset:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	788 tmpSeq += "N"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	789 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	790 tmpSeq += pos
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	791
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	792 return setOfNucleotides, tmpSeq
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	793
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	794
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	795 def getBPDifferenceDistance(stack1, stack2):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	796 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	797 Based on the not identical amount of base pairs within both structure stacks
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	798 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	799 d = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	800 for i in stack1.keys():
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	801 # check base pairs in stack 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	802 if i < stack1[i] and stack1[i] != stack2[i]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	803 d += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	804 # check base pairs in stack 2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	805 for i in stack2.keys():
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	806 if i < stack2[i] and stack1[i] != stack2[i]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	807 d += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	808 return d
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	809
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	810
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	811 def getStructuralDistance(target_structure, Cseq, path, RNAfold, verbose, LP, BP, RNAfold_pattern, IUPAC_compatibles, degreeOfSequenceInducement, pseudoknots, strategy):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	812 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	813 Calculator for Structural Distance
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	814 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	815 # fold the current solution's sequence to obtain the structure
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	816
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	817 current_structure = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	818
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	819 if pseudoknots:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	820 current_structure = getPKStructure(path,strategy)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	821 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	822 RNAfold_match = RNAfold_pattern.match(consult_RNAfold(path, RNAfold))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	823 current_structure = RNAfold_match.group(1)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	824
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	825 # generate the current structure's base-pair stack
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	826 bp = getbpStack(current_structure)[0]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	827 # add case-dependend structural constraints in case of lonley basepairs formation
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	828 tmp_target_structure_bp = getbpStack(target_structure)[0]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	829
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	830 for lp in LP:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	831 if bp[lp] == LP[lp]: # if the base pair is within the current solution structure, re-add the basepair into the constraint structure.
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	832 #tmp_target_structure[lp] = "("
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	833 #tmp_target_structure[LP[lp]] = ")"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	834 tmp_target_structure_bp[lp] = LP[lp]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	835 tmp_target_structure_bp[LP[lp]] = lp
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	836
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	837 # REMOVE BLOCK CONSTRAINT AND SUBSTITUTE IT WITH SINGLE STRAND INFORMATION repsective with brackets, if allowed base pairs occure
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	838 # check for all allowed implicit constraint block declarators
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	839 for c in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	840 occurances = []
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	841 for m in re.finditer(c, target_structure): # search for a declarator in the requested structure
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	842 occurances.append(m.start()) # save the corresponding index
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	843
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	844 # transform declarator into single stranded request
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	845 for i in occurances:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	846 #tmp_target_structure[i] = "."
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	847 tmp_target_structure_bp[i] = i
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	848 # infer a base pair within the block declarated positions, if the current structure provides it.
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	849 for i in occurances:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	850 for j in occurances:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	851 if i < j:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	852 if bp[i] == j:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	853 #tmp_target_structure[i] = "("
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	854 #tmp_target_structure[bp[i]] = ")"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	855
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	856 tmp_target_structure_bp[i] = bp[i]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	857 tmp_target_structure_bp[bp[i]] = i
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	858
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	859 # CHECK FOR SEQUENCE CONSTRAINT WHICH INDUCES STRUCTURE CONSTRAINT IN THE MOMENTARY SITUATION
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	860 #print "Checking Cseq influence and it's induced basepairs..."
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	861 IUPACinducers, tmp_Cseq = getInducingSequencePositions(Cseq, degreeOfSequenceInducement)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	862 if len(Cseq.strip("N")) > 0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	863 #print "Processing Cseq influence"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	864 # Iterate over all positions within the Base Pair stack
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	865 for i in BP: # Check for each base index i
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	866
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	867 if i < bp[i]: # if the current index is samller that the affiliated in the basepair stack of the current solution
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	868
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	869 bp_j = bp[i] # Actual j index of the current solution
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	870 BP_j = BP[i][1][0] # j index of the requested structure
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	871 if (i != bp_j and i == BP_j and BP[i][0] in IUPACinducers ): # if i pairs with some other base in the current structure, and i is requested single stranded and the Sequence constraint is allowed to induce...
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	872 if (BP[bp_j][1][0] == bp_j and BP[bp_j][0] in IUPACinducers):# If position j is requested singlestranded and position j nucleotide can induce base pairs
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	873 #if isCompatible(bp[i][0], bp[i][1][1], IUPAC_compatibles): # If both nucleotides, i and j are actually compatible
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	874 #tmp_target_structure[i] = "("
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	875 #tmp_target_structure[bp_j] = ")"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	876
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	877 tmp_target_structure_bp[i] = bp[i]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	878 tmp_target_structure_bp[bp_j] = i
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	879
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	880 #tts = "".join(tmp_target_structure)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	881 dsreg = getBPDifferenceDistance(tmp_target_structure_bp, bp)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	882
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	883 # CHECK FOR ALL DETERMINED LONELY BASE PAIRS (i<j), if they are formed
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	884 failLP = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	885 for lp in LP:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	886
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	887 if bp[lp] != LP[lp]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	888
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	889 isComp = isCompatible(path[lp],path[LP[lp]], IUPAC_compatibles)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	890 isStru = isStructureCompatible(lp, LP[lp] ,bp)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	891 if not ( isStru and isStru ): # check if the bases at the specific positions are compatible and check if the
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	892 # basepair can be formed according to pseudoknot free restriction. If one fails, a penalty distance is raised for that base pair
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	893 failLP += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	894
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	895 #print dsreg, failLP, float(len(tmp_target_structure_bp))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	896 dsLP = float(failLP)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	897
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	898 return (dsreg + dsLP) /float(len(tmp_target_structure_bp))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	899
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	900
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	901 def getGC(sequence):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	902 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	903 Calculate GC content of a sequence
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	904 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	905 GC = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	906 for nt in sequence:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	907 if nt == "G" or nt == "C":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	908 GC = GC + 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	909 GC = GC/float(len(sequence))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	910 return GC
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	911
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	912
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	913 def getGCDistance(tGC, gc2, L):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	914 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	915 Calculate the pseudo GC content distance
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	916 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	917 nt_coeff = L * tGC
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	918 pc_nt = (1/float(L))*100
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	919 #
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	920 d = gc2 - tGC
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	921 d = d * 100
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	922
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	923 f = math.floor(nt_coeff)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	924 c = math.ceil(nt_coeff)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	925
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	926 if d < 0: #
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	927 #print "case x",(abs(nt_coeff - f)), pc_nt, (abs(nt_coeff - f)) * pc_nt,
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	928 d = d + (abs(nt_coeff - f)) * pc_nt
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	929 elif d > 0: # case y
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	930 #print "case y", abs(nt_coeff - c), pc_nt, abs(nt_coeff - c) * pc_nt,
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	931 d = d - abs(nt_coeff - c) * pc_nt
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	932 elif d == 0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	933 pass
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	934
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	935 d = round(d, 7)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	936 #d = max(0, abs(d)- ( max ( abs( math.ceil(nt_coeff)-(nt_coeff)) , abs(math.floor(nt_coeff)-(nt_coeff)) )/L)*100 )
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	937 return abs(d)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	938
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	939
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	940 def getSequenceEditDistance(SC, path):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	941 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	942 Calculate sequence edit distance of a solution to the constraint
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	943 """#
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	944 IUPAC = {"A":"A", "C":"C", "G":"G", "U":"U", "R":"AG", "Y":"CU", "S":"GC", "W":"AU","K":"GU", "M":"AC", "B":"CGU", "D":"AGU", "H":"ACU", "V":"ACG", "N":"ACGU"}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	945 edit = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	946 for i in xrange(len(SC)):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	947 if path[i] not in IUPAC[SC[i]]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	948 edit += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	949 return edit/float(len(path))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	950
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	951
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	952
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	953 def getTransitions(p):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	954 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	955 Retreive transitions of a specific path/sequence
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	956 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	957 transitions = []
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	958 for pos in xrange(len(p)):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	959 if pos == 0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	960 transitions.append(str(pos) + "." + p[pos])
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	961
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	962 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	963 insert = p[pos-1] + p[pos]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	964 transitions.append(str(pos) + "." + insert)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	965
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	966 return transitions
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	967
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	968
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	969 def evaporate(t, er):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	970 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	971 Evaporate the terrain's pheromone trails
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	972 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	973 terr, BP = t
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	974 c = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	975 for key in terr:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	976 p,l,c = terr[key]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	977 p *= (1-er)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	978 terr[key] = (p, l, c)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	979
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	980
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	981 def updateValue(distance, correction_term, omega):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	982 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	983 Retrieves a distance dependend pheromone value
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	984 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	985 if correction_term == 0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	986 return 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	987 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	988 if distance == 0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	989 return omega * correction_term
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	990 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	991 return (1/float(distance)) * correction_term
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	992
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	993
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	994 def trailBlaze(p, c_s, s, ds, dgc, dseq, dn, t, correction_terms, BPstack, verbose):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	995 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	996 Pheromone Update function accorinding to the quality of the solution
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	997 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	998 terr, BP = t
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	999 bpstack, LP = getbpStack(c_s)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1000
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1001 struct_correction_term , GC_correction_term, seq_correction_term = correction_terms
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1002 omega = 2.23
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1003
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1004 bs = updateValue(ds, struct_correction_term, omega)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1005 bGC = updateValue(dgc, GC_correction_term, omega)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1006 if dseq != "n.a.":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1007 bSeq = updateValue(dseq, seq_correction_term, omega)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1008 d = bs + bGC + bSeq
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1009 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1010 d = bs + bGC
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1011 transitions = getTransitions(p)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1012
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1013 for trans in xrange(len(transitions)): # for each transition in the path
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1014 id1 = int(transitions[trans].split(".")[0])
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1015 tar_id2 = int(BPstack[id1][1][0]) # getting requested position id2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1016 curr_id2 = int(bpstack[id1]) # getting the current situation
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1017 multiplicator = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1018 if tar_id2 == curr_id2 and id1 != tar_id2 and id1 != curr_id2: # case of a base pair, having both brackets on the correct position
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1019 multiplicator = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1020 elif tar_id2 == curr_id2 and id1 == tar_id2 and id1 == curr_id2: # case of a single stranded base in both structures
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1021 multiplicator = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1022 p, l, c = terr[transitions[trans]] # getting the pheromone and the length value of the single path transition
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1023 p += d * multiplicator
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1024 terr[transitions[trans]] = (p, l, c) # updating the values wihtin the terrain's
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1025 t = (terr, BP)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1026
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1027
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1028 def updateTerrain(p, c_s, s, ds, dgc, dseq, dn, t, er, correction_terms, BPstack, verbose, ant_count):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1029 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1030 General updating function
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1031 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1032 evaporate(t,er)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1033 trailBlaze(p, c_s, s, ds, dgc, dseq, dn, t, correction_terms, BPstack, verbose)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1034
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1035
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1036 def getUsedTime(start_time):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1037 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1038 Return the used time between -start time- and now.
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1039 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1040 end_time = time.time()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1041 return end_time - start_time
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1042
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1043
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1044 def good2Go(SC, L, CC, STR):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1045 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1046 Check, if all input is correct and runnable
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1047 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1048 if (SC == 1 and L == 1 and CC == 1 and STR == 1):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1049 return True
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1050 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1051 print SC,L,CC,STR
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1052 return False
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1053
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1054
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1055 def getPathFromSelection( aps, s, terrain, alpha, beta, RNAfold, RNAfold_pattern, GC, SC, LP, verbose, IUPAC_compatibles, degreeOfSequenceInducement, IUPAC_reverseComplements, IUPAC, pseudoknots, strategy):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1056 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1057 Returns the winning path from a selection of pathes...
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1058 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1059 terr, BPs = terrain
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1060 win_path = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1061 for i in xrange(aps):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1062 # Generate Sequence
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1063 path = getPath(s, terr, BPs, alpha, beta, IUPAC, IUPAC_reverseComplements)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1064 # Measure sequence features and transform them into singular distances
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1065 distance_structural = float(getStructuralDistance(s, SC , path, RNAfold, verbose, LP, BPs, RNAfold_pattern, IUPAC_compatibles, degreeOfSequenceInducement, pseudoknots, strategy))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1066 distance_GC = float(getGCDistance(GC,getGC(path), len(path)))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1067 distance_seq = float(getSequenceEditDistance(SC, path))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1068 # Calculate Distance Score
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1069 D = distance_structural + distance_GC + distance_seq
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1070
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1071 # SELECT THE BEST-OUT-OF-k-SOLUTIONS according to distance score
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1072 if i == 0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1073 win_path = (path, D, distance_structural, distance_GC, distance_seq)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1074 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1075 if D < win_path[1]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1076 win_path = (path, D, distance_structural, distance_GC, distance_seq)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1077 return win_path
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1078
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1079
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1080 def substr(x, string, subst):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1081 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1082 Classical substring function
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1083 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1084 s1 = string[:x-1]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1085
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1086 s2 = string[x-1:x]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1087 s3 = string[x:]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1088 #s2 = s[x+len(string)-x-1:]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1089
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1090 return s1 + subst + s3
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1091
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1092
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1093 def inConvergenceCorridor(d_struct, d_gc, BS_d_struct, BS_d_gc):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1094 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1095 Check if a solutions qualities are within the convergence corridor
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1096 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1097 struct_var = ((BS_d_struct/float(4)) + 3 ) * 4
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1098 gc_var = (BS_d_gc + 1/float(100) * 5) + BS_d_gc + 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1099
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1100 if d_struct <= struct_var and d_gc <= gc_var:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1101 return True
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1102 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1103 return False
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1104
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1105 def getGCSamplingValue(GC, tGCmax, tGCvar):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1106 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1107 Returns a suitable GC value, dependend on the user input: Either returning the single GC value,
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1108 which the user entered, or a smpled GC value
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1109 from a designated distribution in it's interavals
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1110 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1111 returnval = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1112 if tGCmax == -1.0 and tGCvar == -1.0: # regular plain tGC value as requested
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1113 return GC
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1114 elif tGCmax != -1.0 and tGCvar == -1.0: # uniform distribution tGC value sampling
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1115 if GC < tGCmax:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1116 tmp_GC = tGCmax
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1117 tGCmax = GC
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1118 GC = tmp_GC
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1119 while returnval <= 0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1120 returnval = float(numpy.random.uniform(low=GC, high=tGCmax, size=1))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1121 return returnval
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1122 elif tGCmax == -1.0 and tGCvar != -1.0: # normal distribution tGC value sampling
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1123 while returnval <= 0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1124 returnval = float(numpy.random.normal(GC, tGCvar, 1))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1125 return returnval
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1126
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1127
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1128 def reachableGC(C_struct):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1129 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1130 Checks if a demanded GC target content is reachable in dependence with the given sequence constraint.
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1131 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1132 AU = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1133 for i in C_struct:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1134 if i == "A" or i == "U":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1135 AU += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1136 maxGC = 1 - (AU / float(len(C_struct))) # 1 - min_GC
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1137 return maxGC
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1138
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1139
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1140 def runColony(s, SC, objective_to_target_distance, GC, alpha, beta, evaporation_rate, correction_terms, verbose, IUPAC, IUPAC_compatibles, degreeOfSequenceInducement, IUPAC_reverseComplements, termination_convergence, convergence_count, reset_limit, improve, temperature, paramFile, pseudoknots, strategy):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1141 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1142 Execution function of a single ant colony finding one solution sequence
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1143 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1144 retString = ""
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1145 retString2 = []
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1146 BPstack, LP = getBPStack(s, SC)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1147
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1148 rGC = reachableGC(SC)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1149 GC_message = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1150 if GC > rGC:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1151 print >> sys.stderr, "WARNING: Chosen target GC %s content is not reachable due to sequence constraint! Sequence Constraint GC-content is: %s" % (GC, rGC)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1152 GC = rGC
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1153
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1154 # Initial Constraint Checks prior to execution
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1155 STR = isValidStructure(s)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1156 START_SC , SC = checkSequenceConstraint(str(SC))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1157 START_LENGTH = checkSimilarLength(str(s), str(SC))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1158 START_constraint_compatibility , CompReport = checkConstaintCompatibility(BPstack, SC, IUPAC_compatibles)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1159
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1160 g2g = good2Go(START_SC, START_LENGTH, START_constraint_compatibility, STR)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1161 if (g2g == 1):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1162 start_time = time.time()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1163 max_time = 600 # seconds
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1164
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1165
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1166
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1167
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1168 ####
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1169 # INITIALIZATION OF THE RNA TOOLs
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1170 #
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1171 RNAfold = init_RNAfold(213, temperature, paramFile)
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1172 #RNAdistance = init_RNAdistance()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1173 RNAfold_pattern = re.compile('.+\n([.()]+)\s.+')
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1174 #RNAdist_pattern = re.compile('.*\s([\d]+)')
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1175 #
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1176 ####
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1177
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1178 terrain = initTerrain(s)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1179 #print len(terrain),
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1180 terrain = applyTerrainModification(terrain, s, GC, SC, BPstack, IUPAC, IUPAC_compatibles, IUPAC_reverseComplements)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1181 #print len(terrain[0])
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1182 #printTerrain(terrain)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1183 #exit(0)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1184 global_ant_count = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1185 global_best_ants = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1186 criterion = False
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1187 met = True
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1188 ant_no = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1189 prev_res = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1190 seq = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1191
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1192 counter = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1193
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1194 dstruct_log = []
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1195 dGC_log = []
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1196
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1197
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1198 distance_structural = 1000
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1199 distance_GC = 1000
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1200 distance_seq = 1000
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1201
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1202 convergence = convergence_count
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1203 convergence_counter = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1204
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1205 resets = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1206
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1207 path = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1208 curr_structure = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1209
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1210 Dscore = 100000
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1211 distance_structural = 10000
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1212 distance_GC = 10000
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1213 distance_seq = 10000
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1214 best_solution = (path, curr_structure, Dscore, distance_structural, distance_GC, distance_seq)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1215 best_solution_local = (path, curr_structure, Dscore, distance_structural, distance_GC, distance_seq)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1216
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1217 best_solution_since = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1218
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1219 ants_per_selection = 10
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1220 if len(LP) > 0 :
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1221 for lp in LP:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1222 s = substr(lp + 1, s, ".")
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1223 s = substr(LP[lp] + 1, s, ".")
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1224
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1225 init = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1226 while criterion != met and getUsedTime(start_time) < max_time:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1227 iteration_start = time.time()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1228 global_ant_count += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1229 global_best_ants += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1230
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1231 path_info = getPathFromSelection(ants_per_selection, s, terrain, alpha, beta, RNAfold, RNAfold_pattern, GC, SC, LP, verbose, IUPAC_compatibles, degreeOfSequenceInducement, IUPAC_reverseComplements, IUPAC, pseudoknots, strategy)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1232
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1233 distance_structural_prev = distance_structural
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1234 distance_GC_prev = distance_GC
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1235 distance_seq_prev = distance_seq
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1236
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1237 path, Dscore , distance_structural, distance_GC, distance_seq = path_info
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1238 curr_structure = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1239 if pseudoknots:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1240 curr_structure = getPKStructure(path, strategy)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1241 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1242 curr_structure = getRNAfoldStructure(path, RNAfold)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1243
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1244 curr_solution = (path,curr_structure, Dscore, distance_structural, distance_GC, distance_seq)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1245 # BEST SOLUTION PICKING
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1246 if improve == "h": # hierarchical check
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1247 # for the global best solution
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1248 if distance_structural < best_solution[3] or (distance_structural == best_solution[3] and distance_GC < best_solution[4]):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1249 best_solution = curr_solution
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1250 ant_no = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1251 # for the local (reset) best solution
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1252 if distance_structural < best_solution_local[3] or (distance_structural == best_solution_local[3] and distance_GC < best_solution_local[4]):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1253 best_solution_local = curr_solution
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1254
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1255 elif improve == "s": #score based check
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1256 # store best global solution
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1257 if Dscore < best_solution[2]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1258 best_solution = curr_solution
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1259 ant_no = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1260 # store best local solution for this reset
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1261 if Dscore < best_solution_local[2]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1262 best_solution_local = curr_solution
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1263
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1264 # OLD ' BEST SOLUTION ' PICKING
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1265 # if Dscore < best_solution[2]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1266 # best_solution = (path,curr_structure, Dscore, distance_structural, distance_GC, distance_seq)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1267 #
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1268 # if Dscore < best_solution_local[2]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1269 # best_solution_local = (path,curr_structure, Dscore, distance_structural, distance_GC, distance_seq)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1270
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1271
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1272 distance_DN = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1273
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1274 if verbose:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1275 print "SCORE " + str(Dscore) + " Resets " + str(resets) + " #Ant " + str(global_ant_count) + " out of " + str(ants_per_selection) + " cc " + str(convergence_counter)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1276
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1277 print s, " <- target struct"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1278 print best_solution[0] , " <- BS since ", str(best_solution_since), "Size of Terrrain:", len(terrain[0])
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1279 print best_solution[1] , " <- BS Dscore " + str(best_solution[2]) + " ds " + str(best_solution[3]) + " dGC " + str(best_solution[4]) + " dseq " + str(best_solution[5])+ " LP " + str(len(LP)) + " <- best solution stats"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1280 print curr_structure, " <- CS"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1281 print path,
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1282 print " <- CS", "Dscore", str(Dscore), "ds", distance_structural, "dGC", distance_GC, "GC", getGC(path)*100, "Dseq", distance_seq
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1283
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1284 #### UPDATING THE TERRAIN ACCORDING TO THE QUALITY OF THE CURRENT BESTO-OUT-OF-k SOLUTION
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1285 updateTerrain(path, curr_structure, s, distance_structural,distance_GC, distance_seq, distance_DN, terrain, evaporation_rate, correction_terms, BPstack, verbose, global_ant_count)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1286 ####
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1287 if verbose: print "Used time for one iteration", time.time() - iteration_start
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1288
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1289
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1290 # CONVERGENCE AND TERMINATION CRITERION MANAGEMENT
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1291 #print distance_structural, distance_GC, best_solution_local[3], best_solution_local[4]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1292 if inConvergenceCorridor(curr_solution[3], curr_solution[4], best_solution_local[3], best_solution_local[4]):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1293 convergence_counter += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1294 if distance_structural_prev == distance_structural and distance_GC_prev == distance_GC:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1295 convergence_counter += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1296
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1297 if best_solution[3] == objective_to_target_distance:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1298 if best_solution[4] == 0.0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1299 break
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1300 ant_no = ant_no + 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1301 convergence_counter -= 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1302 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1303 ant_no = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1304
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1305
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1306 if ant_no == termination_convergence or resets >= reset_limit or global_ant_count >= 100000 or best_solution_since == 5:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1307 break
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1308
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1309 # RESET
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1310 if ant_no < termination_convergence and convergence_counter >= convergence:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1311
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1312 terrain = initTerrain(s)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1313 terrain = applyTerrainModification(terrain, s, GC, SC, BPstack, IUPAC, IUPAC_compatibles, IUPAC_reverseComplements)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1314 criterion = False
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1315 met = True
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1316 ant_no = 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1317 prev_res = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1318 pre_path = "_" * len(s)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1319 path = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1320 curr_structure = ""
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1321 counter = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1322 Dscore = 100000
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1323 distance_structural = 1000
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1324 distance_GC = 1000
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1325 distance_seq = 1000
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1326 best_solution_local = (path, curr_structure, Dscore, distance_structural, distance_GC, distance_seq)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1327 convergence = convergence_count
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1328 convergence_counter = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1329
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1330 if resets == 0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1331 sentinel_solution = best_solution
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1332 best_solution_since += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1333 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1334 if best_solution[2] < sentinel_solution[2]:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1335 sentinel_solution = best_solution
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1336 best_solution_since = 0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1337 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1338 best_solution_since += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1339
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1340 resets += 1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1341
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1342 duration = getUsedTime(start_time)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1343
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1344 retString += "\|Ants:" + str(global_ant_count)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1345 retString += "\|Resets:" + str(resets) + "/" + str(reset_limit)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1346 retString += "\|AntsTC:" + str(termination_convergence)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1347 retString += "\|CC:" + str(convergence_count)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1348 retString += "\|IP:" + str(improve)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1349 retString += "\|BSS:" + str(best_solution_since)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1350 #if GC_message != "":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1351 # retString += GC_message + "\n"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1352
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1353 sequence = best_solution[0]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1354 struct = best_solution[1]
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1355
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1356 retString += "\|LP:" + str(len(LP))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1357 retString += "\|ds:" + str(getStructuralDistance(s,SC, sequence, RNAfold, verbose, LP, BPstack, RNAfold_pattern, IUPAC_compatibles, degreeOfSequenceInducement, pseudoknots, strategy))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1358 retString += "\|dGC:" + str(best_solution[4])
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1359 retString += "\|GC:" + str(getGC(sequence)*100)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1360 retString += "\|dseq:" + str(getSequenceEditDistance(SC, sequence))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1361 retString += "\|L:" + str(len(sequence))
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1362 retString += "\|Time:" + str(duration)
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1363
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1364 retString2.append(struct)
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1365 retString2.append(sequence)
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1366
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1367 # CLOSING THE PIPES TO THE PROGRAMS
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1368 RNAfold.communicate()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1369 #RNAdistance.communicate()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1370
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1371 else: # Structural premisses are not met, htherefore the program will halt with a failure message
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1372 retString += "\nSome mistake detected\n"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1373 retString += "SequenceConstraintCheck: " + str(START_SC) + "\nSequenceConstraint: " + str(SC) + "\nLengthCheck: " + str(START_LENGTH) + "\nConstraintCompatibility: " + str(START_constraint_compatibility)+ "\n" + CompReport + "\n"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1374
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1375 return (retString, retString2)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1376
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1377 def findSequence(structure, Cseq, tGC, colonies, name, alpha, beta, evaporation_rate, struct_correction_term, GC_correction_term, seq_correction_term, degreeOfSequenceInducement, file_id, verbose, output_verbose, tGCmax, tGCvar, termination_convergence, convergence_count, reset_limit, improve, seed, temperature, paramFile, pseudoknots, strategy, useGU, return_mod = False):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1378 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1379 MAIN antaRNA - ant assembled RNA
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1380 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1381
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1382 if seed != "none":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1383 random.seed(seed)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1384
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1385 if Cseq == "":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1386 sequenceconstraint = "N" * len(structure)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1387 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1388 sequenceconstraint = str(Cseq)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1389
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1390 alpha = float(alpha)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1391 beta = float(beta)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1392 tGC = float(tGC)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1393 evaporation_rate = float(evaporation_rate)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1394 struct_correction_term = float(struct_correction_term)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1395 GC_correction_term = float(GC_correction_term)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1396 seq_correction_term = float(seq_correction_term)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1397 colonies = int(colonies)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1398 file_id = str(file_id)
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1399 tmp_verbose = verbose
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1400 tmp_output_verbose = output_verbose
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1401 verbose = tmp_output_verbose # Due to later change, this is a twistaround and a switching of purpose
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1402 output_verbose = tmp_verbose # Due to later change, this is a twistaround and a switching of purpose
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1403 correction_terms = struct_correction_term, GC_correction_term, seq_correction_term
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1404 temperature = float(temperature)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1405 print_to_STDOUT = (file_id == "STDOUT")
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1406
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1407 useGU = useGU
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1408
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1409 if return_mod == False:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1410 if print_to_STDOUT == False:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1411 outfolder = '/'.join(file_id.strip().split("/")[:-1])
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1412 curr_dir = os.getcwd()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1413 if not os.path.exists(outfolder):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1414 os.makedirs(outfolder)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1415 os.chdir(outfolder)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1416
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1417
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1418 sequenceconstraint = transform(sequenceconstraint)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1419 ###############################################
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1420
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1421 # Allowed deviation from the structural target:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1422 objective_to_target_distance = 0.0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1423
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1424 # Loading the IUPAC copatibilities of nuleotides and their abstract representing symbols
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1425 IUPAC = {"A":"A", "C":"C", "G":"G", "U":"U", "R":"AG", "Y":"CU", "S":"GC", "W":"AU","K":"GU", "M":"AC", "B":"CGU", "D":"AGU", "H":"ACU", "V":"ACG", "N":"ACGU"}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1426 IUPAC_compatibles = loadIUPACcompatibilities(IUPAC, useGU)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1427
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1428 IUPAC_reverseComplements = {}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1429 if useGU == False: ## Without the GU basepair
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1430 IUPAC_reverseComplements = {"A":"U", "C":"G", "G":"C", "U":"A", "R":"UC", "Y":"AG", "S":"GC", "W":"UA","K":"CA", "M":"UG", "B":"AGC", "D":"ACU", "H":"UGA", "V":"UGC", "N":"ACGU"}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1431 else: ## allowing the GU basepair
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1432 IUPAC_reverseComplements = {"A":"U", "C":"G", "G":"UC", "U":"AG", "R":"UC", "Y":"AG", "S":"UGC", "W":"UAG","K":"UCAG", "M":"UG", "B":"AGCU", "D":"AGCU", "H":"UGA", "V":"UGC", "N":"ACGU"}
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1433
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1434 result = []
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1435 for col in xrange(colonies):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1436 # Checking the kind of taget GC value should be used
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1437 GC = getGCSamplingValue(tGC, tGCmax, tGCvar)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1438
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1439 # Actual execution of a ant colony procesdure
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1440 output_v, output_w = runColony(structure, sequenceconstraint, objective_to_target_distance, GC, alpha, beta, evaporation_rate, correction_terms, verbose, IUPAC, IUPAC_compatibles, degreeOfSequenceInducement, IUPAC_reverseComplements, termination_convergence, convergence_count, reset_limit, improve, temperature, paramFile, pseudoknots, strategy)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1441
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1442 # Post-Processing the output of a ant colony procedure
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1443 line = ">" + name + str(col)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1444 if output_verbose:
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1445 line += "\|Cstr:" + structure + "\|Cseq:" + sequenceconstraint + "\|Alpha:" + str(alpha) + "\|Beta:" + str(beta) + "\|tGC:" + str(GC) + "\|ER:" + str(evaporation_rate) + "\|Struct_CT:" + str(struct_correction_term) + "\|GC_CT:" + str(GC_correction_term) + "\|Seq_CT:" + str(seq_correction_term) + output_v + "\n" + "\n".join(output_w)
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1446 else:
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1447 line += "\n" + output_w[1]
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1448 if return_mod == False:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1449 if print_to_STDOUT:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1450 print line
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1451 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1452 if col == 0:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1453 print2file(file_id, line, 'w')
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1454 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1455 print2file(file_id, line, 'a')
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1456 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1457 result.append(line)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1458
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1459 if return_mod == True:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1460 return result
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1461 if print_to_STDOUT == False:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1462 os.chdir(curr_dir)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1463
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1464 def execute(args):
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1465 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1466 CHECK AND PARSE THE COMMAND LINE STUFF
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1467 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1468
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1469 # Checking the arguments, parsed from the shell
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1470 ###############################################
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1471 name = args.name
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1472 structure = args.Cstr
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1473
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1474 if args.Cseq == "":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1475 sequenceconstraint = "N" * len(structure)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1476 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1477 sequenceconstraint = args.Cseq
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1478
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1479 seed = args.seed
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1480
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1481
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1482 alpha = args.alpha
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1483 beta = args.beta
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1484 tGC = args.tGC
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1485 if tGC < 0 or tGC > 1:
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1486 print "Error: Chosen tGC not in range [0,1]"
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1487 exit(1)
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1488 evaporation_rate = args.ER
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1489 struct_correction_term = args.Cstrweight
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1490 GC_correction_term = args.Cgcweight
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1491 seq_correction_term = args.Cseqweight
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1492 colonies = args.noOfColonies
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1493 degreeOfSequenceInducement = args.level
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1494 file_id = args.output_file
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1495 verbose = args.verbose
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1496 output_verbose = args.output_verbose
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1497
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1498 tGCmax = args.tGCmax
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1499 tGCvar = args.tGCvar
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1500
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1501 termination_convergence = args.antsTerConv
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1502 convergence_count = args.ConvergenceCount
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1503 temperature = args.temperature
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1504 reset_limit = args.Resets
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1505
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1506 improve = args.improve_procedure
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1507
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1508 ### RNAfold parameterfile
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1509 paramFile = args.paramFile
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1510
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1511 # Using the pkiss program under user changeable parameters
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1512 pseudoknots = args.pseudoknots
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1513
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1514 # Loading the optimized parameters for pseudoknots and ignore user input
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1515 if args.pseudoknot_parameters:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1516 alpha = 1.0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1517 beta = 0.1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1518 evaporation_rate = 0.2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1519 struct_correction_term = 0.1
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1520 GC_correction_term = 1.0
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1521 seq_correction_term = 0.5
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1522 termination_convergence = 50
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1523 convergence_count = 100
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1524
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1525
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1526 strategy = args.strategy
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1527 useGU = args.useGUBasePair
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1528
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1529 checkForViennaTools()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1530 if pseudoknots:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1531 checkForpKiss()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1532 findSequence(structure, sequenceconstraint, tGC, colonies, name, alpha, beta, evaporation_rate, struct_correction_term, GC_correction_term, seq_correction_term, degreeOfSequenceInducement, file_id, verbose, output_verbose, tGCmax, tGCvar, termination_convergence, convergence_count, reset_limit, improve, seed, temperature, paramFile, pseudoknots, strategy, useGU)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1533
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1534
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1535 def exe():
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1536 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1537 MAIN EXECUTABLE WHICH PARSES THE INPUT LINE
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1538 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1539
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1540 argument_parser = argparse.ArgumentParser(
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1541 description = """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1542
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1543 #########################################################################
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1544 # antaRNA - ant assembled RNA #
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1545 # -> Ant Colony Optimized RNA Sequence Design #
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1546 # ------------------------------------------------------------ #
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1547 # Robert Kleinkauf (c) 2015 #
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1548 # Bioinformatics, Albert-Ludwigs University Freiburg, Germany #
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1549 #########################################################################
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1550
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1551 - For antaRNA only the VIENNNA RNA Package must be installed on your linux system.
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1552 antaRNA will only check, if the executables of RNAfold and RNAdistance of the ViennaRNA package can be found. If those programs are
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1553 not installed correctly, no output will be generated, an also no warning will be prompted.
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1554 So the binary path of the Vienna Tools must be set up correctly in your system's PATH variable in order to run antaRNA correctly!
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1555
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1556 - antaRNA was only tested under Linux.
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1557
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1558 - For questions and remarks please feel free to contact us at http://www.bioinf.uni-freiburg.de/
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1559
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1560 """,
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1561
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1562 epilog = """
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1563 Example calls:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1564 python antaRNA.py --Cstr "...(((...)))..." --tGC 0.5 -n 2
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1565 python antaRNA.py --Cstr ".........AAA(((...)))AAA........." --tGC 0.5 -n 10 --output_file /path/to/antaRNA_TESTRUN -ov
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1566 python antaRNA.py --Cstr "BBBBB....AAA(((...)))AAA....BBBBB" --Cseq "NNNNANNNNNCNNNNNNNNNNNGNNNNNNUNNN" --tGC 0.5 -n 10
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1567
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1568 #########################################################################
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1569 # --- Hail to the Queen!!! All power to the swarm!!! --- #
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1570 #########################################################################
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1571 """,
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1572 #formatter_class=RawTextHelpFormatter
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1573 )
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1574
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1575 # mandatorys
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1576 argument_parser.add_argument("-Cstr", "--Cstr", help="Structure constraint using RNA dotbracket notation with fuzzy block constraint. \n(TYPE: %(type)s)\n\n", type=str, required=True)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1577 argument_parser.add_argument("-tGC", "--tGC", help="Objective target GC content in [0,1].\n(TYPE: %(type)s)\n\n", type=float, required=True)
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1578 argument_parser.add_argument("-n", "--noOfColonies", help="Number of sequences which shall be produced. \n(TYPE: %(type)s)\n\n\n\n", type=int, default=1)
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1579 argument_parser.add_argument("-GU", "--useGUBasePair", help="Allowing GU base pairs. \n\n", action="store_true")
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1580
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1581 argument_parser.add_argument("-s", "--seed", help = "Provides a seed value for the used pseudo random number generator.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=str, default="none")
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1582 argument_parser.add_argument("-ip", "--improve_procedure", help = "Select the improving method. h=hierarchical, s=score_based.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=str, default="s")
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1583 argument_parser.add_argument("-r", "--Resets", help = "Amount of maximal terrain resets, until the best solution is retuned as solution.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=int, default=5)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1584 argument_parser.add_argument("-CC", "--ConvergenceCount", help = "Delimits the convergence count criterion for a reset.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=int, default=130)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1585 argument_parser.add_argument("-aTC", "--antsTerConv", help = "Delimits the amount of internal ants for termination convergence criterion for a reset.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=int, default=50)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1586
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1587 argument_parser.add_argument("-p", "--pseudoknots", help = "Switch to pseudoknot based prediction using pKiss. Check the pseudoknot parameter usage!!!\n\n", action="store_true")
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1588 argument_parser.add_argument("-pkPar", "--pseudoknot_parameters", help = "Enable optimized parameters for the usage of pseudo knots (Further parameter input ignored).\n\n", action="store_true")
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1589 argument_parser.add_argument("--strategy", help = "Defining the pKiss folding strategy.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=str, default="A")
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1590
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1591 # Mutual Exclusiv target GC distribution variables
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1592 #tGCgroup = argument_parser.add_mutually_exclusive_group()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1593 argument_parser.add_argument("-tGCmax", "--tGCmax", help = "Provides a maximum tGC value [0,1] for the case of uniform distribution sampling. The regular tGC value serves as minimum value.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=-1.0)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1594 argument_parser.add_argument("-tGCvar", "--tGCvar", help = "Provides a tGC variance (sigma square) for the case of normal distribution sampling. The regular tGC value serves as expectation value (mu).\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=-1.0)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1595
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1596 argument_parser.add_argument("-t", "--temperature", help = "Provides a temperature for the folding algorithms.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=37.0)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1597 argument_parser.add_argument("-P", "--paramFile", help = "Changes the energy parameterfile of RNAfold. If using this explicitly, please provide a suitable energy file delivered by RNAfold. \n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=str, default="")
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1598 argument_parser.add_argument("-of","--output_file", help="Provide a path and an output file, e.g. \"/path/to/the/target_file\". \n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=str, default="STDOUT")
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1599 argument_parser.add_argument("-Cseq", "--Cseq", help="Sequence constraint using RNA nucleotide alphabet {A,C,G,U} and wild-card \"N\". \n(TYPE: %(type)s)\n\n", type=str, default = "")
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1600 argument_parser.add_argument("-l", "--level", help="Sets the level of allowed influence of sequence constraint on the structure constraint [0:no influence; 3:extensive influence].\n(TYPE: %(type)s)\n\n", type=int, default = 1)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1601 argument_parser.add_argument("--name", help="Defines a name which is used in the sequence output. \n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=str, default="antaRNA_")
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1602 argument_parser.add_argument("-a", "--alpha", help="Sets alpha, probability weight for terrain pheromone influence. [0,1] \n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=1.0)
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1603 argument_parser.add_argument("-b", "--beta", help="Sets beta, probability weight for terrain path influence. [0,1]\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=1.0)
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1604 argument_parser.add_argument("-er", "--ER", help="Pheromone evaporation rate. \n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=0.2)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1605 argument_parser.add_argument("-Cstrw", "--Cstrweight", help="Structure constraint quality weighting factor. [0,1]\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=0.5)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1606 argument_parser.add_argument("-Cgcw", "--Cgcweight", help="GC content constraint quality weighting factor. [0,1]\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=5.0)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1607 argument_parser.add_argument("-Cseqw", "--Cseqweight", help="Sequence constraint quality weighting factor. [0,1]\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n\n", type=float, default=1.0)
7 2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1608 argument_parser.add_argument("-ov", "--output_verbose", help="Displayes intermediate output.\n\n", action="store_true")
2f68c8d1c080 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 92a4a51ff5405ac0ba2a35bddb33608b99b61593-dirty rnateam parents: 6 diff changeset	1609 argument_parser.add_argument("-v", "--verbose", help="Prints additional features and stats to the headers of the produced sequences. Also adds the structure of the sequence.\n\n", action="store_true")
0 3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1610
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1611 args = argument_parser.parse_args()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1612
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1613 execute(args)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1614
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1615 def checkForViennaTools():
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1616 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1617 Checking for the presence of the Vienna tools in the system by which'ing for RNAfold and RNAdistance
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1618 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1619 RNAfold_output = subprocess.Popen(["which", "RNAfold"], stdout=subprocess.PIPE).communicate()[0].strip()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1620 if len(RNAfold_output) > 0 and RNAfold_output.find("found") == -1 and RNAfold_output.find(" no ") == -1:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1621 return True
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1622 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1623 print "It seems the Vienna RNA Package is not installed on your machine. Please do so!"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1624 print "You can get it at http://www.tbi.univie.ac.at/"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1625 exit(0)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1626
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1627
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1628 def checkForpKiss():
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1629 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1630 Checking for the presence of pKiss
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1631 """
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1632 pKiss_output = subprocess.Popen(["which", "pKiss"], stdout=subprocess.PIPE).communicate()[0].strip()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1633 if len(pKiss_output) > 0 and pKiss_output.find("found") == -1 and pKiss_output.find(" no ") == -1:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1634 return True
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1635 else:
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1636 print "It seems that pKiss is not installed on your machine. Please do so!"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1637 print "You can get it at http://bibiserv2.cebitec.uni-bielefeld.de/pkiss"
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1638 exit(0)
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1639
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1640
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1641
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1642 if __name__ == "__main__":
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1643
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1644 exe()
3fde35e023f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty rnateam parents: diff changeset	1645

Mercurial > repos > rnateam > antarna

annotate antaRNA.py @ 18:a9a0fb585968 draft default tip