mira4_assembler: tools/mira4_0/mira4

annotate tools/mira4_0/mira4_convert.py @ 39:bbf14bb9607b draft default tip

planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6

author	peterjc
date	Mon, 03 Jun 2019 13:29:00 -0400
parents	cee8f9005e43
children

rev	line source
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	1 #!/usr/bin/env python
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	2 """A simple wrapper script to call MIRA and collect its output.
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	3
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	4 This focuses on the miraconvert binary.
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	5 """
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	6
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	7 from __future__ import print_function
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	8
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	9 import os
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	10 import shutil
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	11 import subprocess
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	12 import sys
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	13
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	14 from optparse import OptionParser
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	15
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	16 try:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	17 from io import BytesIO
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	18 except ImportError:
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	19 # Should we worry about Python 2.5 or older?
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	20 from StringIO import StringIO as BytesIO
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	21
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	22 # Do we need any PYTHONPATH magic?
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	23 from mira4_make_bam import depad
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	24
35 259891fce7fd planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412 peterjc parents: 34 diff changeset	25 WRAPPER_VER = "0.0.11" # Keep in sync with the XML file
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	26
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	27
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	28 def run(cmd):
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	29 # Avoid using shell=True when we call subprocess to ensure if the Python
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	30 # script is killed, so too is the child process.
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	31 try:
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	32 child = subprocess.Popen(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	33 cmd, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	34 )
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	35 except Exception as err:
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	36 sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	37 # Use .communicate as can get deadlocks with .wait(),
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	38 stdout, stderr = child.communicate()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	39 return_code = child.returncode
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	40 if return_code:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	41 cmd_str = " ".join(cmd) # doesn't quote spaces etc
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	42 if stderr and stdout:
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	43 sys.exit(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	44 "Return code %i from command:\n%s\n\n%s\n\n%s"
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	45 % (return_code, cmd_str, stdout, stderr)
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	46 )
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	47 else:
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	48 sys.exit(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	49 "Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr)
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	50 )
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	51
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	52
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	53 def get_version(mira_binary):
38 cee8f9005e43 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 206259620376b322fc8ed99a6efdd3712f38764b peterjc parents: 35 diff changeset	54 """Run MIRA to find its version number."""
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	55 # At the commend line I would use: mira -v \| head -n 1
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	56 # however there is some pipe error when doing that here.
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	57 cmd = [mira_binary, "-v"]
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	58 try:
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	59 child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	60 except Exception as err:
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	61 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	62 sys.exit(1)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	63 ver, tmp = child.communicate()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	64 del child
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	65 return ver.split("\n", 1)[0].strip()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	66
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	67
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	68 # Parse Command Line
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	69 usage = (
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	70 """Galaxy MIRA4 wrapper script v%s - use as follows:
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	71
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	72 $ python mira4_convert.py ...
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	73
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	74 This will run the MIRA miraconvert binary and collect its output files as directed.
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	75 """
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	76 % WRAPPER_VER
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	77 )
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	78 parser = OptionParser(usage=usage)
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	79 parser.add_option(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	80 "--input", dest="input", default=None, metavar="FILE", help="MIRA input filename"
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	81 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	82 parser.add_option(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	83 "-x", "--min_length", dest="min_length", default="0", help="Minimum contig length"
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	84 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	85 parser.add_option(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	86 "-y",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	87 "--min_cover",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	88 dest="min_cover",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	89 default="0",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	90 help="Minimum average contig coverage",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	91 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	92 parser.add_option(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	93 "-z", "--min_reads", dest="min_reads", default="0", help="Minimum reads per contig"
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	94 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	95 parser.add_option(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	96 "--maf", dest="maf", default="", metavar="FILE", help="MIRA MAF output filename"
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	97 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	98 parser.add_option(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	99 "--ace", dest="ace", default="", metavar="FILE", help="ACE output filename"
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	100 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	101 parser.add_option(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	102 "--bam", dest="bam", default="", metavar="FILE", help="Unpadded BAM output filename"
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	103 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	104 parser.add_option(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	105 "--fasta",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	106 dest="fasta",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	107 default="",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	108 metavar="FILE",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	109 help="Unpadded FASTA output filename",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	110 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	111 parser.add_option(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	112 "--cstats",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	113 dest="cstats",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	114 default="",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	115 metavar="FILE",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	116 help="Contig statistics filename",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	117 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	118 parser.add_option(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	119 "-v",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	120 "--version",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	121 dest="version",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	122 default=False,
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	123 action="store_true",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	124 help="Show version and quit",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	125 )
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	126 options, args = parser.parse_args()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	127 if args:
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	128 sys.exit("Expected options (e.g. --input example.maf), not arguments")
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	129
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	130 input_maf = options.input
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	131 out_maf = options.maf
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	132 out_bam = options.bam
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	133 out_fasta = options.fasta
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	134 out_ace = options.ace
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	135 out_cstats = options.cstats
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	136
35 259891fce7fd planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412 peterjc parents: 34 diff changeset	137 if "MIRA4" in os.environ:
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	138 mira_path = os.environ["MIRA4"]
35 259891fce7fd planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412 peterjc parents: 34 diff changeset	139 mira_convert = os.path.join(mira_path, "miraconvert")
259891fce7fd planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412 peterjc parents: 34 diff changeset	140 if not os.path.isfile(mira_convert):
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	141 sys.exit(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	142 "Missing miraconvert under $MIRA4, %r\nFolder contained: %s"
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	143 % (mira_convert, ", ".join(os.listdir(mira_path)))
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	144 )
35 259891fce7fd planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412 peterjc parents: 34 diff changeset	145 else:
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	146 sys.stderr.write(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	147 "DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n"
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	148 )
35 259891fce7fd planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412 peterjc parents: 34 diff changeset	149 mira_path = None
259891fce7fd planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412 peterjc parents: 34 diff changeset	150 mira_convert = "miraconvert"
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	151
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	152 mira_convert_ver = get_version(mira_convert)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	153 if not mira_convert_ver.strip().startswith("4.0"):
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	154 sys.exit(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	155 "This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_convert_ver, mira_convert)
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	156 )
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	157 if options.version:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	158 print("%s, MIRA wrapper version %s" % (mira_convert_ver, WRAPPER_VER))
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	159 sys.exit(0)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	160
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	161 if not input_maf:
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	162 sys.exit("Input MIRA file is required")
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	163 elif not os.path.isfile(input_maf):
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	164 sys.exit("Missing input MIRA file: %r" % input_maf)
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	165
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	166 if not (out_maf or out_bam or out_fasta or out_ace or out_cstats):
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	167 sys.exit("No output requested")
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	168
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	169
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	170 def check_min_int(value, name):
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	171 try:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	172 i = int(value)
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	173 except ValueError:
fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	174 sys.exit("Bad %s setting, %r" % (name, value))
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	175 if i < 0:
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	176 sys.exit("Negative %s setting, %r" % (name, value))
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	177 return i
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	178
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	179
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	180 min_length = check_min_int(options.min_length, "minimum length")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	181 min_cover = check_min_int(options.min_cover, "minimum cover")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	182 min_reads = check_min_int(options.min_reads, "minimum reads")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	183
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	184 # TODO - Run MIRA in /tmp or a configurable directory?
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	185 # Currently Galaxy puts us somewhere safe like:
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	186 # /opt/galaxy-dist/database/job_working_directory/846/
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	187 temp = "."
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	188
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	189
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	190 cmd_list = [mira_convert]
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	191 if min_length:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	192 cmd_list.extend(["-x", str(min_length)])
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	193 if min_cover:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	194 cmd_list.extend(["-y", str(min_cover)])
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	195 if min_reads:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	196 cmd_list.extend(["-z", str(min_reads)])
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	197 cmd_list.extend(["-f", "maf", input_maf, os.path.join(temp, "converted")])
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	198 if out_maf:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	199 cmd_list.append("maf")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	200 if out_bam:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	201 cmd_list.append("samnbb")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	202 if not out_fasta:
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	203 # Need this for samtools depad
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	204 out_fasta = os.path.join(temp, "depadded.fasta")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	205 if out_fasta:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	206 cmd_list.append("fasta")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	207 if out_ace:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	208 cmd_list.append("ace")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	209 if out_cstats:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	210 cmd_list.append("cstats")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	211 run(cmd_list)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	212
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	213
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	214 def collect(old, new):
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	215 if not os.path.isfile(old):
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	216 sys.exit("Missing expected output file %s" % old)
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	217 shutil.move(old, new)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	218
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	219
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	220 if out_maf:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	221 collect(os.path.join(temp, "converted.maf"), out_maf)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	222 if out_fasta:
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	223 # Can we look at the MAF file to see if there are multiple strains?
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	224 old = os.path.join(temp, "converted_AllStrains.unpadded.fasta")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	225 if os.path.isfile(old):
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	226 collect(old, out_fasta)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	227 else:
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	228 # Might the output be filtered down to zero contigs?
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	229 old = os.path.join(temp, "converted.fasta")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	230 if not os.path.isfile(old):
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	231 sys.exit("Missing expected output FASTA file")
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	232 elif os.path.getsize(old) == 0:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	233 print("Warning - no contigs (harsh filters?)")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	234 collect(old, out_fasta)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	235 else:
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	236 sys.exit("Missing expected output FASTA file (only generic file present)")
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	237 if out_ace:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	238 collect(os.path.join(temp, "converted.maf"), out_ace)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	239 if out_cstats:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	240 collect(os.path.join(temp, "converted_info_contigstats.txt"), out_cstats)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	241
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	242 if out_bam:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	243 assert os.path.isfile(out_fasta)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	244 old = os.path.join(temp, "converted.samnbb")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	245 if not os.path.isfile(old):
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	246 old = os.path.join(temp, "converted.sam")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	247 if not os.path.isfile(old):
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	248 sys.exit("Missing expected intermediate file %s" % old)
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	249 h = BytesIO()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	250 msg = depad(out_fasta, old, out_bam, h)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	251 if msg:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	252 print(msg)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	253 print(h.getvalue())
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	254 h.close()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	255 sys.exit(1)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	256 h.close()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	257 if out_fasta == os.path.join(temp, "depadded.fasta"):
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	258 # Not asked for by Galaxy, no longer needed
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	259 os.remove(out_fasta)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	260
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	261 if min_length or min_cover or min_reads:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	262 print("Filtered.")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	263 else:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	264 print("Converted.")

Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4_0/mira4_convert.py @ 39:bbf14bb9607b draft default tip