mira4_assembler: tools/mira4_0/mira4.py annotate

annotate tools/mira4_0/mira4.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
38 cee8f9005e43 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 206259620376b322fc8ed99a6efdd3712f38764b peterjc parents: 35 diff changeset	2 """A simple wrapper script to call MIRA and collect its output."""
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	3
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	4 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	5
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	6 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	7 import shutil
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	8 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	9 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	10 import tempfile
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	11 import time
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
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	13 from optparse import OptionParser
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	14
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 # Do we need any PYTHONPATH magic?
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	16 from mira4_make_bam import make_bam
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	17
35 259891fce7fd planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412 peterjc parents: 34 diff changeset	18 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	19
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	20
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	21 def get_version(mira_binary):
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 """Run MIRA to find its version number."""
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	23 # 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	24 # however there is some pipe error when doing that here.
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	25 cmd = [mira_binary, "-v"]
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	26 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	27 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	28 cmd,
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	29 universal_newlines=True,
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	30 stdout=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	31 stderr=subprocess.STDOUT,
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	32 )
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	33 except Exception as err:
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	34 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	35 sys.exit(1)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	36 ver, tmp = child.communicate()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	37 del child
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	38 return ver.split("\n", 1)[0].strip()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	39
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	40
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	41 # 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	42 usage = (
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	43 """Galaxy MIRA4 wrapper script v%s - use as follows:
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	44
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	45 $ python mira4.py ...
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	46
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	47 This will run the MIRA 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	48 """
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	49 % 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	50 )
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	51 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	52 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	53 "-m",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	54 "--manifest",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	55 dest="manifest",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	56 default=None,
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	57 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	58 help="MIRA manifest filename",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	59 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	60 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	61 "--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	62 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	63 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	64 "--bam",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	65 dest="bam",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	66 default="-",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	67 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	68 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	69 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	70 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	71 "--fasta",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	72 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	73 default="-",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	74 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	75 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	76 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	77 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	78 "--log",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	79 dest="log",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	80 default="-",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	81 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	82 help="MIRA logging 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	83 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	84 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	85 "-v",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	86 "--version",
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	87 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	88 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	89 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	90 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	91 )
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	92 options, args = parser.parse_args()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	93 manifest = options.manifest
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	94 out_maf = options.maf
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	95 out_bam = options.bam
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	96 out_fasta = options.fasta
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	97 out_log = options.log
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	98
35 259891fce7fd planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412 peterjc parents: 34 diff changeset	99 if "MIRA4" in os.environ:
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	100 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	101 mira_binary = os.path.join(mira_path, "mira")
259891fce7fd planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412 peterjc parents: 34 diff changeset	102 if not os.path.isfile(mira_binary):
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	103 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	104 "Missing mira 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	105 % (mira_binary, ", ".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	106 )
35 259891fce7fd planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412 peterjc parents: 34 diff changeset	107 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	108 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	109 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	110 "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	111 % (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	112 )
35 259891fce7fd planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412 peterjc parents: 34 diff changeset	113 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	114 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	115 "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	116 )
35 259891fce7fd planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412 peterjc parents: 34 diff changeset	117 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	118 mira_binary = "mira"
259891fce7fd planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412 peterjc parents: 34 diff changeset	119 mira_convert = "miraconvert"
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	120
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	121 mira_ver = get_version(mira_binary)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	122 if not mira_ver.strip().startswith("4.0"):
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	123 sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_binary))
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	124 mira_convert_ver = get_version(mira_convert)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	125 if not mira_convert_ver.strip().startswith("4.0"):
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	126 sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_convert))
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	127 if options.version:
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	128 print("%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER))
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	129 if mira_ver != mira_convert_ver:
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	130 print("WARNING: miraconvert %s" % mira_convert_ver)
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	131 sys.exit(0)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	132
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	133 if not manifest:
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	134 sys.exit("Manifest is required")
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	135 elif not os.path.isfile(manifest):
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	136 sys.exit("Missing input MIRA manifest file: %r" % manifest)
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	137
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	138
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	139 try:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	140 threads = int(os.environ.get("GALAXY_SLOTS", "1"))
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	141 except ValueError:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	142 threads = 1
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	143 assert 1 <= threads, threads
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	144
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	145
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	146 def override_temp(manifest):
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	147 """Override ``-DI:trt=/tmp`` in manifest with environment variable.
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	148
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	149 Currently MIRA 4 does not allow envronment variables like ``$TMP``
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	150 inside the manifest, which is a problem if you need to override
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	151 the default at run time.
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	152
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	153 The tool XML will ``/tmp`` and we replace that here with
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	154 ``tempfile.gettempdir()`` which will respect $TMPDIR, $TEMP, $TMP
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	155 as explained in the Python standard library documentation:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	156 http://docs.python.org/2/library/tempfile.html#tempfile.tempdir
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	157
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	158 By default MIRA 4 would write its temporary files within the output
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	159 folder, which is a problem if that is a network drive.
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 handle = open(manifest, "r")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	162 text = handle.read()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	163 handle.close()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	164
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	165 # At time of writing, this is at the end of a file,
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	166 # but could be followed by a space in future...
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	167 text = text.replace("-DI:trt=/tmp", "-DI:trt=" + tempfile.gettempdir())
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	168
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	169 # Want to try to ensure this gets written to disk before MIRA attempts
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	170 # to open it - any networked file system may impose a delay...
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	171 handle = open(manifest, "w")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	172 handle.write(text)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	173 handle.flush()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	174 os.fsync(handle.fileno())
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	175 handle.close()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	176
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	177
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	178 def log_manifest(manifest):
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	179 """Write the manifest file to stderr."""
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	180 sys.stderr.write("\n%s\nManifest file\n%s\n" % ("=" * 60, "=" * 60))
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	181 with open(manifest) as h:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	182 for line in h:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	183 sys.stderr.write(line)
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 sys.stderr.write("\n%s\nEnd of manifest\n%s\n" % ("=" * 60, "=" * 60))
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	185
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	186
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	187 def collect_output(temp, name, handle):
38 cee8f9005e43 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 206259620376b322fc8ed99a6efdd3712f38764b peterjc parents: 35 diff changeset	188 """Move files to the output filenames (global variables)."""
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	189 f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	190 if not os.path.isdir(f):
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	191 log_manifest(manifest)
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	192 sys.exit("Missing output folder")
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	193 if not os.listdir(f):
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	194 log_manifest(manifest)
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	195 sys.exit("Empty output folder")
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	196 missing = []
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	197
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	198 old_maf = "%s/%s_out.maf" % (f, name)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	199 if not os.path.isfile(old_maf):
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	200 # Triggered extractLargeContigs.sh?
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	201 old_maf = "%s/%s_LargeContigs_out.maf" % (f, name)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	202
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 # De novo or single strain mapping,
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	204 old_fasta = "%s/%s_out.unpadded.fasta" % (f, name)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	205 ref_fasta = "%s/%s_out.padded.fasta" % (f, name)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	206 if not os.path.isfile(old_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	207 # Mapping (StrainX versus reference) or de novo
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	208 old_fasta = "%s/%s_out_StrainX.unpadded.fasta" % (f, name)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	209 ref_fasta = "%s/%s_out_StrainX.padded.fasta" % (f, name)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	210 if not os.path.isfile(old_fasta):
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	211 old_fasta = "%s/%s_out_ReferenceStrain.unpadded.fasta" % (f, name)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	212 ref_fasta = "%s/%s_out_ReferenceStrain.padded.fasta" % (f, name)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	213
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	214 missing = False
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	215 for old, new in [(old_maf, out_maf), (old_fasta, out_fasta)]:
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	216 if not os.path.isfile(old):
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	217 missing = True
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	218 elif not new or new == "-":
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	219 handle.write("Ignoring %s\n" % old)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	220 else:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	221 handle.write("Capturing %s\n" % old)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	222 shutil.move(old, new)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	223 if missing:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	224 log_manifest(manifest)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	225 sys.stderr.write("Contents of %r:\n" % f)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	226 for filename in sorted(os.listdir(f)):
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	227 sys.stderr.write("%s\n" % filename)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	228
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	229 # For mapping mode, probably most people would expect a BAM file
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	230 # using the reference FASTA file...
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	231 if out_bam and out_bam != "-":
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	232 if out_maf and out_maf != "-":
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	233 msg = make_bam(mira_convert, out_maf, ref_fasta, out_bam, handle)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	234 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	235 # Not collecting the MAF file, use original location
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	236 msg = make_bam(mira_convert, old_maf, ref_fasta, out_bam, handle)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	237 if msg:
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	238 sys.exit(msg)
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	239
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	240
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	241 def clean_up(temp, name):
38 cee8f9005e43 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 206259620376b322fc8ed99a6efdd3712f38764b peterjc parents: 35 diff changeset	242 """Remove temp files."""
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	243 folder = "%s/%s_assembly" % (temp, name)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	244 if os.path.isdir(folder):
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	245 shutil.rmtree(folder)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	246
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	247
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	248 # 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	249 # 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	250 # /opt/galaxy-dist/database/job_working_directory/846/
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	251 temp = "."
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	252
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	253 name = "MIRA"
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	254
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	255 override_temp(manifest)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	256
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	257 start_time = time.time()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	258 cmd_list = [mira_binary, "-t", str(threads), manifest]
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	259 cmd = " ".join(cmd_list)
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 assert os.path.isdir(temp)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	262 d = "%s_assembly" % name
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	263 # This can fail on my development machine if stale folders exist
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	264 # under Galaxy's .../database/job_working_directory/ tree:
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	265 assert not os.path.isdir(d), "Path %r already exists:\n%s" % (d, os.path.abspath(d))
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	266 try:
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	267 # Check path access
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	268 os.mkdir(d)
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	269 except Exception as err:
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	270 log_manifest(manifest)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	271 sys.stderr.write("Error making directory %s\n%s" % (d, err))
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	272 sys.exit(1)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	273
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	274 # print(os.path.abspath("."))
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	275 # print(cmd)
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	276
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	277 if out_log and out_log != "-":
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	278 handle = open(out_log, "w")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	279 else:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	280 handle = open(os.devnull, "w")
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	281 handle.write(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	282 "======================== MIRA manifest (instructions) ========================\n"
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	283 )
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	284 m = open(manifest, "rU")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	285 for line in m:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	286 handle.write(line)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	287 m.close()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	288 del m
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	289 handle.write("\n")
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	290 handle.write(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	291 "============================ Starting MIRA now ===============================\n"
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	292 )
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	293 handle.flush()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	294 try:
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	295 # Run MIRA
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	296 child = subprocess.Popen(cmd_list, stdout=handle, 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	297 except Exception as err:
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	298 log_manifest(manifest)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	299 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (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	300 # TODO - call clean up?
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	301 handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	302 handle.close()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	303 sys.exit(1)
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	304 # Use .communicate as can get deadlocks with .wait(),
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	305 stdout, stderr = child.communicate()
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	306 assert not stdout and not stderr # Should be empty as sent to handle
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	307 run_time = time.time() - start_time
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	308 return_code = child.returncode
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	309 handle.write("\n")
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	310 handle.write(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	311 "============================ MIRA has finished ===============================\n"
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	312 )
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	313 handle.write("MIRA took %0.2f hours\n" % (run_time / 3600.0))
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	314 if return_code:
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	315 print("MIRA took %0.2f hours" % (run_time / 3600.0))
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	316 handle.write("Return error code %i from command:\n" % return_code)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	317 handle.write(cmd + "\n")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	318 handle.close()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	319 clean_up(temp, name)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	320 log_manifest(manifest)
31 fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	321 sys.stderr.write("Return error code %i from command:\n" % return_code)
fd95aaef8818 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c peterjc parents: 25 diff changeset	322 sys.stderr.write(cmd + "\n")
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	323 sys.exit(return_code)
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	324 handle.flush()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	325
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	326 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	327 handle.write("\n")
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	328 handle.write(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	329 "====================== Extract Large Contigs failed ==========================\n" # noqa: E501
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	330 )
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	331 e = open("MIRA_assembly/MIRA_d_results/ec.log", "rU")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	332 for line in e:
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	333 handle.write(line)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	334 e.close()
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	335 handle.write(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	336 "============================ (end of ec.log) =================================\n" # noqa: E501
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	337 )
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	338 handle.flush()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	339
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	340 # print("Collecting output...")
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	341 start_time = time.time()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	342 collect_output(temp, name, handle)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	343 collect_time = time.time() - start_time
39 bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	344 handle.write(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	345 "MIRA took %0.2f hours; collecting output %0.2f minutes\n"
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	346 % (run_time / 3600.0, collect_time / 60.0)
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	347 )
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	348 print(
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	349 "MIRA took %0.2f hours; collecting output %0.2f minutes\n"
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	350 % (run_time / 3600.0, collect_time / 60.0)
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6 peterjc parents: 38 diff changeset	351 )
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	352
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	353 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	354 # Treat as an error, but doing this AFTER collect_output
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	355 sys.stderr.write("Extract Large Contigs failed\n")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	356 handle.write("Extract Large Contigs failed\n")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	357 handle.close()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	358 sys.exit(1)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	359
32 56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6 peterjc parents: 31 diff changeset	360 # print "Cleaning up..."
25 55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	361 clean_up(temp, name)
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	362
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	363 handle.write("\nDone\n")
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	364 handle.close()
55ae131c5862 v0.0.8 - renamed folder, added note about mirabait peterjc parents: diff changeset	365 print("Done")

Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4_0/mira4.py @ 39:bbf14bb9607b draft default tip