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annotate cuffcompare_wrapper.py @ 9:e66b9b5b8580 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
author devteam
date Sun, 19 Feb 2017 12:12:05 -0500
parents 1322b73ffe44
children
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1 #!/usr/bin/env python
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2
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3 # Supports Cuffcompare versions v1.3.0 and newer.
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4
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5 import optparse
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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6 import os
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7 import shutil
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8 import subprocess
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9 import sys
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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10 import tempfile
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11
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12
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13 def stop_err(msg):
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14 sys.stderr.write('%s\n' % msg)
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15 sys.exit()
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16
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17
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18 def __main__():
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19 parser = optparse.OptionParser()
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20 parser.add_option('-r', dest='ref_annotation', help='An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below.')
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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21 parser.add_option('-R', action="store_true", dest='ignore_nonoverlap_reference', help='If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the transcripts accuracy file')
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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22 parser.add_option('-Q', action="store_true", dest='ignore_nonoverlap_transfrag', help='If -r was specified, this option causes cuffcompare to consider only the input transcripts that overlap any of the reference transcripts (Sp correction); Warning: this will discard all "novel" loci!)')
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24 parser.add_option('-s', dest='use_seq_data', action="store_true", help='Causes cuffcompare to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.')
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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26 parser.add_option('-M', action="store_true", dest='discard_single_exon_all', help='discard (ignore) single-exon transfrags and reference transcript')
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27 parser.add_option('-N', action="store_true", dest='discard_single_exon_ref', help='discard (ignore) single-exon reference transcripts')
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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28 parser.add_option('-e', dest='max_dist_exon', help='Max. Distance for assessing exon accuracy" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100')
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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29 parser.add_option('-d', dest='max_dist_group', help='Max.Distance for transcript grouping" help="max. distance (range) for grouping transcript start sites. Default: 100')
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30 parser.add_option('-F', action="store_true", dest='discard_redundant_intron_transfrags', help='Discard intron-redundant transfrags if they share the 5-prime end (if they differ only at the 3-prime end)')
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31
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32 # Wrapper / Galaxy options.
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33 parser.add_option('', '--index', dest='index', help='The path of the reference genome')
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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34 parser.add_option('', '--ref_file', dest='ref_file', help='The reference dataset from the history')
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35
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36 # Outputs.
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37 parser.add_option('', '--combined-transcripts', dest='combined_transcripts')
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38
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39 (options, args) = parser.parse_args()
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40
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41 # Set/link to sequence file.
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42 if options.use_seq_data:
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43 if options.ref_file:
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44 # Sequence data from history.
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45 # Create symbolic link to ref_file so that index will be created in working directory.
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46 seq_path = "ref.fa"
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47 os.symlink(options.ref_file, seq_path)
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48 else:
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49 if not os.path.exists(options.index):
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50 stop_err('Reference genome %s not present, request it by reporting this error.' % options.index)
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51 seq_path = options.index
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52
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53 # Build command.
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54
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55 # Base.
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56 cmd = "cuffcompare -o cc_output "
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57
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58 # Add options.
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59 if options.ref_annotation:
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60 cmd += " -r %s " % options.ref_annotation
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61 if options.ignore_nonoverlap_reference:
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62 cmd += " -R "
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63 if options.ignore_nonoverlap_transfrag:
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64 cmd += " -Q "
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65 if options.use_seq_data:
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66 cmd += " -s %s " % seq_path
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67 if options.discard_single_exon_all:
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68 cmd += " -M "
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69 if options.discard_single_exon_ref:
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70 cmd += " -N "
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71 if options.max_dist_exon:
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72 cmd += " -e %i " % int(options.max_dist_exon)
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73 if options.max_dist_group:
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74 cmd += " -d %i " % int(options.max_dist_group)
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75 if options.discard_redundant_intron_transfrags:
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76 cmd += " -F "
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77 # Add input files.
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78
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79 # Need to symlink inputs so that output files are written to the current directory.
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80 for i, arg in enumerate(args):
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81 input_file_name = "./input%i" % (i + 1)
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82 os.symlink(arg, input_file_name)
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83 cmd += "%s " % input_file_name
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84
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85 # Run command.
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86 try:
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87 with tempfile.NamedTemporaryFile(dir=".") as tmp_stderr:
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88 returncode = subprocess.call(args=cmd, stderr=tmp_stderr, shell=True)
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89
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90 # Error checking.
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91 if returncode != 0:
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92 # Get stderr, allowing for case where it's very large.
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93 buffsize = 1048576
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94 stderr = ''
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95 with open(tmp_stderr.name) as tmp_stderr2:
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96 try:
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97 while True:
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98 stderr += tmp_stderr2.read(buffsize)
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99 if not stderr or len(stderr) % buffsize != 0:
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100 break
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101 except OverflowError:
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102 pass
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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103 raise Exception(stderr)
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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104
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105 # Copy outputs.
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1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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106 shutil.move("cc_output.combined.gtf", options.combined_transcripts)
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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107
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108 # check that there are results in the output file
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109 cc_output_fname = "cc_output.stats"
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1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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110 if len(open(cc_output_fname).read().strip()) == 0:
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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111 raise Exception('The main output file is empty, there may be an error with your input file or settings.')
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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112 except Exception as e:
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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113 stop_err('Error running cuffcompare: %s' % e)
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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114
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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115
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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116 if __name__ == "__main__":
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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117 __main__()