Mercurial > repos > peterjc > mira4_assembler
annotate tools/mira4_0/mira4.py @ 33:1291ed21789f draft
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 1d7d466d01b23d03d214e93f1f8efa19cfa18268
| author | peterjc |
|---|---|
| date | Fri, 02 Jun 2017 11:22:01 -0400 |
| parents | 56b421d59805 |
| children | 0785a6537f3e |
| rev | line source |
|---|---|
| 25 | 1 #!/usr/bin/env python |
| 2 """A simple wrapper script to call MIRA and collect its output. | |
| 3 """ | |
|
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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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4 |
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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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5 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
peterjc
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6 |
| 25 | 7 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
parents:
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changeset
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8 import shutil |
| 25 | 9 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
parents:
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changeset
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10 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
parents:
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changeset
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11 import tempfile |
| 25 | 12 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
parents:
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changeset
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13 |
| 25 | 14 from optparse import OptionParser |
| 15 | |
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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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16 # Do we need any PYTHONPATH magic? |
| 25 | 17 from mira4_make_bam import make_bam |
| 18 | |
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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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19 WRAPPER_VER = "0.0.10" # Keep in sync with the XML file |
| 25 | 20 |
| 21 | |
| 22 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
parents:
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changeset
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23 """Run MIRA to find its version number.""" |
| 25 | 24 # At the commend line I would use: mira -v | head -n 1 |
| 25 # however there is some pipe error when doing that here. | |
| 26 cmd = [mira_binary, "-v"] | |
| 27 try: | |
| 28 child = subprocess.Popen(cmd, | |
| 29 stdout=subprocess.PIPE, | |
| 30 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
parents:
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changeset
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31 except Exception as err: |
| 25 | 32 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) |
| 33 sys.exit(1) | |
| 34 ver, tmp = child.communicate() | |
| 35 del child | |
| 36 return ver.split("\n", 1)[0].strip() | |
| 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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changeset
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38 |
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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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39 # Parse Command Line |
| 25 | 40 usage = """Galaxy MIRA4 wrapper script v%s - use as follows: |
| 41 | |
| 42 $ python mira4.py ... | |
| 43 | |
| 44 This will run the MIRA binary and collect its output files as directed. | |
| 45 """ % WRAPPER_VER | |
| 46 parser = OptionParser(usage=usage) | |
| 47 parser.add_option("-m", "--manifest", dest="manifest", | |
| 48 default=None, metavar="FILE", | |
| 49 help="MIRA manifest filename") | |
| 50 parser.add_option("--maf", dest="maf", | |
| 51 default="-", metavar="FILE", | |
| 52 help="MIRA MAF output filename") | |
| 53 parser.add_option("--bam", dest="bam", | |
| 54 default="-", metavar="FILE", | |
| 55 help="Unpadded BAM output filename") | |
| 56 parser.add_option("--fasta", dest="fasta", | |
| 57 default="-", metavar="FILE", | |
| 58 help="Unpadded FASTA output filename") | |
| 59 parser.add_option("--log", dest="log", | |
| 60 default="-", metavar="FILE", | |
| 61 help="MIRA logging output filename") | |
| 62 parser.add_option("-v", "--version", dest="version", | |
| 63 default=False, action="store_true", | |
| 64 help="Show version and quit") | |
| 65 options, args = parser.parse_args() | |
| 66 manifest = options.manifest | |
| 67 out_maf = options.maf | |
| 68 out_bam = options.bam | |
| 69 out_fasta = options.fasta | |
| 70 out_log = options.log | |
| 71 | |
| 72 try: | |
| 73 mira_path = os.environ["MIRA4"] | |
| 74 except KeyError: | |
|
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fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
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changeset
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75 sys.exit("Environment variable $MIRA4 not set") |
| 25 | 76 mira_binary = os.path.join(mira_path, "mira") |
| 77 if not os.path.isfile(mira_binary): | |
|
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fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
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changeset
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78 sys.exit("Missing mira under $MIRA4, %r\nFolder contained: %s" |
| 25 | 79 % (mira_binary, ", ".join(os.listdir(mira_path)))) |
| 80 mira_convert = os.path.join(mira_path, "miraconvert") | |
| 81 if not os.path.isfile(mira_convert): | |
|
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fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
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changeset
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82 sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s" |
| 25 | 83 % (mira_convert, ", ".join(os.listdir(mira_path)))) |
| 84 | |
| 85 mira_ver = get_version(mira_binary) | |
| 86 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
parents:
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changeset
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87 sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_binary)) |
| 25 | 88 mira_convert_ver = get_version(mira_convert) |
| 89 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
parents:
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changeset
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90 sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_convert)) |
| 25 | 91 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
parents:
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changeset
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92 print("%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER)) |
| 25 | 93 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
parents:
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changeset
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94 print("WARNING: miraconvert %s" % mira_convert_ver) |
| 25 | 95 sys.exit(0) |
| 96 | |
| 97 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
peterjc
parents:
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98 sys.exit("Manifest is required") |
| 25 | 99 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
parents:
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changeset
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100 sys.exit("Missing input MIRA manifest file: %r" % manifest) |
| 25 | 101 |
| 102 | |
| 103 try: | |
| 104 threads = int(os.environ.get("GALAXY_SLOTS", "1")) | |
| 105 except ValueError: | |
| 106 threads = 1 | |
| 107 assert 1 <= threads, threads | |
| 108 | |
| 109 | |
| 110 def override_temp(manifest): | |
| 111 """Override ``-DI:trt=/tmp`` in manifest with environment variable. | |
| 112 | |
| 113 Currently MIRA 4 does not allow envronment variables like ``$TMP`` | |
| 114 inside the manifest, which is a problem if you need to override | |
| 115 the default at run time. | |
| 116 | |
| 117 The tool XML will ``/tmp`` and we replace that here with | |
| 118 ``tempfile.gettempdir()`` which will respect $TMPDIR, $TEMP, $TMP | |
| 119 as explained in the Python standard library documentation: | |
| 120 http://docs.python.org/2/library/tempfile.html#tempfile.tempdir | |
| 121 | |
| 122 By default MIRA 4 would write its temporary files within the output | |
| 123 folder, which is a problem if that is a network drive. | |
| 124 """ | |
| 125 handle = open(manifest, "r") | |
| 126 text = handle.read() | |
| 127 handle.close() | |
| 128 | |
|
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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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129 # 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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130 # but could be followed by a space in future... |
| 25 | 131 text = text.replace("-DI:trt=/tmp", "-DI:trt=" + tempfile.gettempdir()) |
| 132 | |
|
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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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133 # 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:
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changeset
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134 # to open it - any networked file system may impose a delay... |
| 25 | 135 handle = open(manifest, "w") |
| 136 handle.write(text) | |
| 137 handle.flush() | |
| 138 os.fsync(handle.fileno()) | |
| 139 handle.close() | |
| 140 | |
| 141 | |
| 142 def log_manifest(manifest): | |
| 143 """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
peterjc
parents:
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changeset
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144 sys.stderr.write("\n%s\nManifest file\n%s\n" % ("=" * 60, "=" * 60)) |
| 25 | 145 with open(manifest) as h: |
| 146 for line in h: | |
| 147 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
parents:
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changeset
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148 sys.stderr.write("\n%s\nEnd of manifest\n%s\n" % ("=" * 60, "=" * 60)) |
| 25 | 149 |
| 150 | |
| 151 def collect_output(temp, name, handle): | |
| 152 """Moves files to the output filenames (global variables).""" | |
| 153 f = "%s/%s_assembly/%s_d_results" % (temp, name, name) | |
| 154 if not os.path.isdir(f): | |
| 155 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
peterjc
parents:
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156 sys.exit("Missing output folder") |
| 25 | 157 if not os.listdir(f): |
| 158 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
peterjc
parents:
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159 sys.exit("Empty output folder") |
| 25 | 160 missing = [] |
| 161 | |
| 162 old_maf = "%s/%s_out.maf" % (f, name) | |
| 163 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
parents:
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164 # Triggered extractLargeContigs.sh? |
| 25 | 165 old_maf = "%s/%s_LargeContigs_out.maf" % (f, name) |
| 166 | |
|
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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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167 # De novo or single strain mapping, |
| 25 | 168 old_fasta = "%s/%s_out.unpadded.fasta" % (f, name) |
| 169 ref_fasta = "%s/%s_out.padded.fasta" % (f, name) | |
| 170 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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changeset
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171 # Mapping (StrainX versus reference) or de novo |
| 25 | 172 old_fasta = "%s/%s_out_StrainX.unpadded.fasta" % (f, name) |
| 173 ref_fasta = "%s/%s_out_StrainX.padded.fasta" % (f, name) | |
| 174 if not os.path.isfile(old_fasta): | |
| 175 old_fasta = "%s/%s_out_ReferenceStrain.unpadded.fasta" % (f, name) | |
| 176 ref_fasta = "%s/%s_out_ReferenceStrain.padded.fasta" % (f, name) | |
| 177 | |
| 178 missing = False | |
| 179 for old, new in [(old_maf, out_maf), | |
| 180 (old_fasta, out_fasta)]: | |
| 181 if not os.path.isfile(old): | |
| 182 missing = True | |
| 183 elif not new or new == "-": | |
| 184 handle.write("Ignoring %s\n" % old) | |
| 185 else: | |
| 186 handle.write("Capturing %s\n" % old) | |
| 187 shutil.move(old, new) | |
| 188 if missing: | |
| 189 log_manifest(manifest) | |
| 190 sys.stderr.write("Contents of %r:\n" % f) | |
| 191 for filename in sorted(os.listdir(f)): | |
| 192 sys.stderr.write("%s\n" % filename) | |
| 193 | |
|
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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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194 # 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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changeset
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195 # using the reference FASTA file... |
| 25 | 196 if out_bam and out_bam != "-": |
| 197 if out_maf and out_maf != "-": | |
| 198 msg = make_bam(mira_convert, out_maf, ref_fasta, out_bam, handle) | |
| 199 else: | |
|
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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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200 # Not collecting the MAF file, use original location |
| 25 | 201 msg = make_bam(mira_convert, old_maf, ref_fasta, out_bam, handle) |
| 202 if msg: | |
|
31
fd95aaef8818
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
peterjc
parents:
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203 sys.exit(msg) |
| 25 | 204 |
|
32
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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205 |
| 25 | 206 def clean_up(temp, name): |
| 207 folder = "%s/%s_assembly" % (temp, name) | |
| 208 if os.path.isdir(folder): | |
| 209 shutil.rmtree(folder) | |
| 210 | |
|
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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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211 |
|
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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212 # TODO - Run MIRA in /tmp or a configurable directory? |
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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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213 # Currently Galaxy puts us somewhere safe like: |
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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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214 # /opt/galaxy-dist/database/job_working_directory/846/ |
| 25 | 215 temp = "." |
| 216 | |
| 217 name = "MIRA" | |
| 218 | |
| 219 override_temp(manifest) | |
| 220 | |
| 221 start_time = time.time() | |
| 222 cmd_list = [mira_binary, "-t", str(threads), manifest] | |
| 223 cmd = " ".join(cmd_list) | |
| 224 | |
| 225 assert os.path.isdir(temp) | |
| 226 d = "%s_assembly" % name | |
|
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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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227 # This can fail on my development machine if stale folders exist |
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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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228 # under Galaxy's .../database/job_working_directory/ tree: |
| 25 | 229 assert not os.path.isdir(d), "Path %r already exists:\n%s" % (d, os.path.abspath(d)) |
| 230 try: | |
|
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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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231 # Check path access |
| 25 | 232 os.mkdir(d) |
|
32
56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents:
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diff
changeset
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233 except Exception as err: |
| 25 | 234 log_manifest(manifest) |
| 235 sys.stderr.write("Error making directory %s\n%s" % (d, err)) | |
| 236 sys.exit(1) | |
| 237 | |
|
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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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238 # print(os.path.abspath(".")) |
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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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239 # print(cmd) |
| 25 | 240 |
| 241 if out_log and out_log != "-": | |
| 242 handle = open(out_log, "w") | |
| 243 else: | |
| 244 handle = open(os.devnull, "w") | |
| 245 handle.write("======================== MIRA manifest (instructions) ========================\n") | |
| 246 m = open(manifest, "rU") | |
| 247 for line in m: | |
| 248 handle.write(line) | |
| 249 m.close() | |
| 250 del m | |
| 251 handle.write("\n") | |
| 252 handle.write("============================ Starting MIRA now ===============================\n") | |
| 253 handle.flush() | |
| 254 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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255 # Run MIRA |
| 25 | 256 child = subprocess.Popen(cmd_list, |
| 257 stdout=handle, | |
| 258 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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259 except Exception as err: |
| 25 | 260 log_manifest(manifest) |
| 261 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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262 # TODO - call clean up? |
| 25 | 263 handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) |
| 264 handle.close() | |
| 265 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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266 # Use .communicate as can get deadlocks with .wait(), |
| 25 | 267 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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268 assert not stdout and not stderr # Should be empty as sent to handle |
| 25 | 269 run_time = time.time() - start_time |
| 270 return_code = child.returncode | |
| 271 handle.write("\n") | |
| 272 handle.write("============================ MIRA has finished ===============================\n") | |
| 273 handle.write("MIRA took %0.2f hours\n" % (run_time / 3600.0)) | |
| 274 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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275 print("MIRA took %0.2f hours" % (run_time / 3600.0)) |
| 25 | 276 handle.write("Return error code %i from command:\n" % return_code) |
| 277 handle.write(cmd + "\n") | |
| 278 handle.close() | |
| 279 clean_up(temp, name) | |
| 280 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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281 sys.stderr.write("Return error code %i from command:\n" % return_code) |
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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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282 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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283 sys.exit(return_code) |
| 25 | 284 handle.flush() |
| 285 | |
| 286 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"): | |
| 287 handle.write("\n") | |
| 288 handle.write("====================== Extract Large Contigs failed ==========================\n") | |
| 289 e = open("MIRA_assembly/MIRA_d_results/ec.log", "rU") | |
| 290 for line in e: | |
| 291 handle.write(line) | |
| 292 e.close() | |
| 293 handle.write("============================ (end of ec.log) =================================\n") | |
| 294 handle.flush() | |
| 295 | |
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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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296 # print("Collecting output...") |
| 25 | 297 start_time = time.time() |
| 298 collect_output(temp, name, handle) | |
| 299 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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300 handle.write("MIRA took %0.2f hours; collecting output %0.2f minutes\n" |
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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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301 % (run_time / 3600.0, collect_time / 60.0)) |
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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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302 print("MIRA took %0.2f hours; collecting output %0.2f minutes\n" |
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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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303 % (run_time / 3600.0, collect_time / 60.0)) |
| 25 | 304 |
| 305 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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306 # Treat as an error, but doing this AFTER collect_output |
| 25 | 307 sys.stderr.write("Extract Large Contigs failed\n") |
| 308 handle.write("Extract Large Contigs failed\n") | |
| 309 handle.close() | |
| 310 sys.exit(1) | |
| 311 | |
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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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312 # print "Cleaning up..." |
| 25 | 313 clean_up(temp, name) |
| 314 | |
| 315 handle.write("\nDone\n") | |
| 316 handle.close() | |
| 317 print("Done") |