Mercurial > repos > peterjc > mira4_assembler
annotate tools/mira4_0/mira4.py @ 38:cee8f9005e43 draft
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 206259620376b322fc8ed99a6efdd3712f38764b
| author | peterjc |
|---|---|
| date | Wed, 11 Jul 2018 12:35:35 -0400 |
| parents | 259891fce7fd |
| children | bbf14bb9607b |
| rev | line source |
|---|---|
| 25 | 1 #!/usr/bin/env python |
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cee8f9005e43
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 206259620376b322fc8ed99a6efdd3712f38764b
peterjc
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changeset
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2 """A simple wrapper script to call MIRA and collect its output.""" |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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3 |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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4 from __future__ import print_function |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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5 |
| 25 | 6 import os |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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7 import shutil |
| 25 | 8 import subprocess |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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changeset
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9 import sys |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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changeset
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10 import tempfile |
| 25 | 11 import time |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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12 |
| 25 | 13 from optparse import OptionParser |
| 14 | |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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15 # Do we need any PYTHONPATH magic? |
| 25 | 16 from mira4_make_bam import make_bam |
| 17 | |
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259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
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18 WRAPPER_VER = "0.0.11" # Keep in sync with the XML file |
| 25 | 19 |
| 20 | |
| 21 def get_version(mira_binary): | |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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22 """Run MIRA to find its version number.""" |
| 25 | 23 # At the commend line I would use: mira -v | head -n 1 |
| 24 # however there is some pipe error when doing that here. | |
| 25 cmd = [mira_binary, "-v"] | |
| 26 try: | |
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0785a6537f3e
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 6405ba93fcec7ea93452bf54d559c7507ee7a57c
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27 child = subprocess.Popen(cmd, universal_newlines=True, |
| 25 | 28 stdout=subprocess.PIPE, |
| 29 stderr=subprocess.STDOUT) | |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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30 except Exception as err: |
| 25 | 31 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) |
| 32 sys.exit(1) | |
| 33 ver, tmp = child.communicate() | |
| 34 del child | |
| 35 return ver.split("\n", 1)[0].strip() | |
| 36 | |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
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changeset
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37 |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
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38 # Parse Command Line |
| 25 | 39 usage = """Galaxy MIRA4 wrapper script v%s - use as follows: |
| 40 | |
| 41 $ python mira4.py ... | |
| 42 | |
| 43 This will run the MIRA binary and collect its output files as directed. | |
| 44 """ % WRAPPER_VER | |
| 45 parser = OptionParser(usage=usage) | |
| 46 parser.add_option("-m", "--manifest", dest="manifest", | |
| 47 default=None, metavar="FILE", | |
| 48 help="MIRA manifest filename") | |
| 49 parser.add_option("--maf", dest="maf", | |
| 50 default="-", metavar="FILE", | |
| 51 help="MIRA MAF output filename") | |
| 52 parser.add_option("--bam", dest="bam", | |
| 53 default="-", metavar="FILE", | |
| 54 help="Unpadded BAM output filename") | |
| 55 parser.add_option("--fasta", dest="fasta", | |
| 56 default="-", metavar="FILE", | |
| 57 help="Unpadded FASTA output filename") | |
| 58 parser.add_option("--log", dest="log", | |
| 59 default="-", metavar="FILE", | |
| 60 help="MIRA logging output filename") | |
| 61 parser.add_option("-v", "--version", dest="version", | |
| 62 default=False, action="store_true", | |
| 63 help="Show version and quit") | |
| 64 options, args = parser.parse_args() | |
| 65 manifest = options.manifest | |
| 66 out_maf = options.maf | |
| 67 out_bam = options.bam | |
| 68 out_fasta = options.fasta | |
| 69 out_log = options.log | |
| 70 | |
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259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
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changeset
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71 if "MIRA4" in os.environ: |
| 25 | 72 mira_path = os.environ["MIRA4"] |
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259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
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changeset
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73 mira_binary = os.path.join(mira_path, "mira") |
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259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
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diff
changeset
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74 if not os.path.isfile(mira_binary): |
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259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
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changeset
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75 sys.exit("Missing mira under $MIRA4, %r\nFolder contained: %s" |
|
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
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changeset
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76 % (mira_binary, ", ".join(os.listdir(mira_path)))) |
|
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
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diff
changeset
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77 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:
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diff
changeset
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78 if not os.path.isfile(mira_convert): |
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259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
34
diff
changeset
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79 sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s" |
|
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
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changeset
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80 % (mira_convert, ", ".join(os.listdir(mira_path)))) |
|
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
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changeset
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81 else: |
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259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
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diff
changeset
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82 sys.stderr.write("DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n") |
|
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
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changeset
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83 mira_path = None |
|
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
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changeset
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84 mira_binary = "mira" |
|
259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
peterjc
parents:
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diff
changeset
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85 mira_convert = "miraconvert" |
| 25 | 86 |
| 87 mira_ver = get_version(mira_binary) | |
| 88 if not mira_ver.strip().startswith("4.0"): | |
|
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fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
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89 sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_binary)) |
| 25 | 90 mira_convert_ver = get_version(mira_convert) |
| 91 if not mira_convert_ver.strip().startswith("4.0"): | |
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fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
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92 sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_convert)) |
| 25 | 93 if options.version: |
|
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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94 print("%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER)) |
| 25 | 95 if mira_ver != mira_convert_ver: |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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96 print("WARNING: miraconvert %s" % mira_convert_ver) |
| 25 | 97 sys.exit(0) |
| 98 | |
| 99 if not manifest: | |
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fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
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100 sys.exit("Manifest is required") |
| 25 | 101 elif not os.path.isfile(manifest): |
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fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
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102 sys.exit("Missing input MIRA manifest file: %r" % manifest) |
| 25 | 103 |
| 104 | |
| 105 try: | |
| 106 threads = int(os.environ.get("GALAXY_SLOTS", "1")) | |
| 107 except ValueError: | |
| 108 threads = 1 | |
| 109 assert 1 <= threads, threads | |
| 110 | |
| 111 | |
| 112 def override_temp(manifest): | |
| 113 """Override ``-DI:trt=/tmp`` in manifest with environment variable. | |
| 114 | |
| 115 Currently MIRA 4 does not allow envronment variables like ``$TMP`` | |
| 116 inside the manifest, which is a problem if you need to override | |
| 117 the default at run time. | |
| 118 | |
| 119 The tool XML will ``/tmp`` and we replace that here with | |
| 120 ``tempfile.gettempdir()`` which will respect $TMPDIR, $TEMP, $TMP | |
| 121 as explained in the Python standard library documentation: | |
| 122 http://docs.python.org/2/library/tempfile.html#tempfile.tempdir | |
| 123 | |
| 124 By default MIRA 4 would write its temporary files within the output | |
| 125 folder, which is a problem if that is a network drive. | |
| 126 """ | |
| 127 handle = open(manifest, "r") | |
| 128 text = handle.read() | |
| 129 handle.close() | |
| 130 | |
|
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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131 # 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
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132 # but could be followed by a space in future... |
| 25 | 133 text = text.replace("-DI:trt=/tmp", "-DI:trt=" + tempfile.gettempdir()) |
| 134 | |
|
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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135 # 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
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136 # to open it - any networked file system may impose a delay... |
| 25 | 137 handle = open(manifest, "w") |
| 138 handle.write(text) | |
| 139 handle.flush() | |
| 140 os.fsync(handle.fileno()) | |
| 141 handle.close() | |
| 142 | |
| 143 | |
| 144 def log_manifest(manifest): | |
| 145 """Write the manifest file to stderr.""" | |
|
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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146 sys.stderr.write("\n%s\nManifest file\n%s\n" % ("=" * 60, "=" * 60)) |
| 25 | 147 with open(manifest) as h: |
| 148 for line in h: | |
| 149 sys.stderr.write(line) | |
|
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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150 sys.stderr.write("\n%s\nEnd of manifest\n%s\n" % ("=" * 60, "=" * 60)) |
| 25 | 151 |
| 152 | |
| 153 def collect_output(temp, name, handle): | |
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cee8f9005e43
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 206259620376b322fc8ed99a6efdd3712f38764b
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154 """Move files to the output filenames (global variables).""" |
| 25 | 155 f = "%s/%s_assembly/%s_d_results" % (temp, name, name) |
| 156 if not os.path.isdir(f): | |
| 157 log_manifest(manifest) | |
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fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
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158 sys.exit("Missing output folder") |
| 25 | 159 if not os.listdir(f): |
| 160 log_manifest(manifest) | |
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31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
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161 sys.exit("Empty output folder") |
| 25 | 162 missing = [] |
| 163 | |
| 164 old_maf = "%s/%s_out.maf" % (f, name) | |
| 165 if not os.path.isfile(old_maf): | |
|
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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166 # Triggered extractLargeContigs.sh? |
| 25 | 167 old_maf = "%s/%s_LargeContigs_out.maf" % (f, name) |
| 168 | |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
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169 # De novo or single strain mapping, |
| 25 | 170 old_fasta = "%s/%s_out.unpadded.fasta" % (f, name) |
| 171 ref_fasta = "%s/%s_out.padded.fasta" % (f, name) | |
| 172 if not os.path.isfile(old_fasta): | |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
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173 # Mapping (StrainX versus reference) or de novo |
| 25 | 174 old_fasta = "%s/%s_out_StrainX.unpadded.fasta" % (f, name) |
| 175 ref_fasta = "%s/%s_out_StrainX.padded.fasta" % (f, name) | |
| 176 if not os.path.isfile(old_fasta): | |
| 177 old_fasta = "%s/%s_out_ReferenceStrain.unpadded.fasta" % (f, name) | |
| 178 ref_fasta = "%s/%s_out_ReferenceStrain.padded.fasta" % (f, name) | |
| 179 | |
| 180 missing = False | |
| 181 for old, new in [(old_maf, out_maf), | |
| 182 (old_fasta, out_fasta)]: | |
| 183 if not os.path.isfile(old): | |
| 184 missing = True | |
| 185 elif not new or new == "-": | |
| 186 handle.write("Ignoring %s\n" % old) | |
| 187 else: | |
| 188 handle.write("Capturing %s\n" % old) | |
| 189 shutil.move(old, new) | |
| 190 if missing: | |
| 191 log_manifest(manifest) | |
| 192 sys.stderr.write("Contents of %r:\n" % f) | |
| 193 for filename in sorted(os.listdir(f)): | |
| 194 sys.stderr.write("%s\n" % filename) | |
| 195 | |
|
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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196 # 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:
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197 # using the reference FASTA file... |
| 25 | 198 if out_bam and out_bam != "-": |
| 199 if out_maf and out_maf != "-": | |
| 200 msg = make_bam(mira_convert, out_maf, ref_fasta, out_bam, handle) | |
| 201 else: | |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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202 # Not collecting the MAF file, use original location |
| 25 | 203 msg = make_bam(mira_convert, old_maf, ref_fasta, out_bam, handle) |
| 204 if msg: | |
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31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
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205 sys.exit(msg) |
| 25 | 206 |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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207 |
| 25 | 208 def clean_up(temp, name): |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 206259620376b322fc8ed99a6efdd3712f38764b
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209 """Remove temp files.""" |
| 25 | 210 folder = "%s/%s_assembly" % (temp, name) |
| 211 if os.path.isdir(folder): | |
| 212 shutil.rmtree(folder) | |
| 213 | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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214 |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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215 # TODO - Run MIRA in /tmp or a configurable directory? |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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216 # Currently Galaxy puts us somewhere safe like: |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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217 # /opt/galaxy-dist/database/job_working_directory/846/ |
| 25 | 218 temp = "." |
| 219 | |
| 220 name = "MIRA" | |
| 221 | |
| 222 override_temp(manifest) | |
| 223 | |
| 224 start_time = time.time() | |
| 225 cmd_list = [mira_binary, "-t", str(threads), manifest] | |
| 226 cmd = " ".join(cmd_list) | |
| 227 | |
| 228 assert os.path.isdir(temp) | |
| 229 d = "%s_assembly" % name | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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230 # This can fail on my development machine if stale folders exist |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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231 # under Galaxy's .../database/job_working_directory/ tree: |
| 25 | 232 assert not os.path.isdir(d), "Path %r already exists:\n%s" % (d, os.path.abspath(d)) |
| 233 try: | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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234 # Check path access |
| 25 | 235 os.mkdir(d) |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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236 except Exception as err: |
| 25 | 237 log_manifest(manifest) |
| 238 sys.stderr.write("Error making directory %s\n%s" % (d, err)) | |
| 239 sys.exit(1) | |
| 240 | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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241 # print(os.path.abspath(".")) |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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242 # print(cmd) |
| 25 | 243 |
| 244 if out_log and out_log != "-": | |
| 245 handle = open(out_log, "w") | |
| 246 else: | |
| 247 handle = open(os.devnull, "w") | |
| 248 handle.write("======================== MIRA manifest (instructions) ========================\n") | |
| 249 m = open(manifest, "rU") | |
| 250 for line in m: | |
| 251 handle.write(line) | |
| 252 m.close() | |
| 253 del m | |
| 254 handle.write("\n") | |
| 255 handle.write("============================ Starting MIRA now ===============================\n") | |
| 256 handle.flush() | |
| 257 try: | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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258 # Run MIRA |
| 25 | 259 child = subprocess.Popen(cmd_list, |
| 260 stdout=handle, | |
| 261 stderr=subprocess.STDOUT) | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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262 except Exception as err: |
| 25 | 263 log_manifest(manifest) |
| 264 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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265 # TODO - call clean up? |
| 25 | 266 handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) |
| 267 handle.close() | |
| 268 sys.exit(1) | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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269 # Use .communicate as can get deadlocks with .wait(), |
| 25 | 270 stdout, stderr = child.communicate() |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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271 assert not stdout and not stderr # Should be empty as sent to handle |
| 25 | 272 run_time = time.time() - start_time |
| 273 return_code = child.returncode | |
| 274 handle.write("\n") | |
| 275 handle.write("============================ MIRA has finished ===============================\n") | |
| 276 handle.write("MIRA took %0.2f hours\n" % (run_time / 3600.0)) | |
| 277 if return_code: | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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278 print("MIRA took %0.2f hours" % (run_time / 3600.0)) |
| 25 | 279 handle.write("Return error code %i from command:\n" % return_code) |
| 280 handle.write(cmd + "\n") | |
| 281 handle.close() | |
| 282 clean_up(temp, name) | |
| 283 log_manifest(manifest) | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
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284 sys.stderr.write("Return error code %i from command:\n" % return_code) |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
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285 sys.stderr.write(cmd + "\n") |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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286 sys.exit(return_code) |
| 25 | 287 handle.flush() |
| 288 | |
| 289 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"): | |
| 290 handle.write("\n") | |
| 291 handle.write("====================== Extract Large Contigs failed ==========================\n") | |
| 292 e = open("MIRA_assembly/MIRA_d_results/ec.log", "rU") | |
| 293 for line in e: | |
| 294 handle.write(line) | |
| 295 e.close() | |
| 296 handle.write("============================ (end of ec.log) =================================\n") | |
| 297 handle.flush() | |
| 298 | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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299 # print("Collecting output...") |
| 25 | 300 start_time = time.time() |
| 301 collect_output(temp, name, handle) | |
| 302 collect_time = time.time() - start_time | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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303 handle.write("MIRA took %0.2f hours; collecting output %0.2f minutes\n" |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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304 % (run_time / 3600.0, collect_time / 60.0)) |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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305 print("MIRA took %0.2f hours; collecting output %0.2f minutes\n" |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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306 % (run_time / 3600.0, collect_time / 60.0)) |
| 25 | 307 |
| 308 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"): | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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309 # Treat as an error, but doing this AFTER collect_output |
| 25 | 310 sys.stderr.write("Extract Large Contigs failed\n") |
| 311 handle.write("Extract Large Contigs failed\n") | |
| 312 handle.close() | |
| 313 sys.exit(1) | |
| 314 | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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315 # print "Cleaning up..." |
| 25 | 316 clean_up(temp, name) |
| 317 | |
| 318 handle.write("\nDone\n") | |
| 319 handle.close() | |
| 320 print("Done") |