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annotate cuffcompare_wrapper.py @ 8:1322b73ffe44 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author devteam
date Tue, 07 Feb 2017 18:38:41 -0500
parents 8e534225baa9
children e66b9b5b8580
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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
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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
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10 import tempfile
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11
8
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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.')
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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')
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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')
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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 # output version # of tool
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42 try:
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43 with tempfile.NamedTemporaryFile() as tmp_stdout:
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44 returncode = subprocess.call(args='cuffcompare 2>&1', stdout=tmp_stdout, shell=True)
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45 stdout = None
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46 with open(tmp_stdout.name) as tmp_stdout2:
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47 for line in tmp_stdout2:
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48 if line.lower().find('cuffcompare v') >= 0:
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49 stdout = line.strip()
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50 break
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51 if stdout:
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52 sys.stdout.write('%s\n' % stdout)
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53 else:
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54 raise Exception
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55 except:
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56 sys.stdout.write('Could not determine Cuffcompare version\n')
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57
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58 # Set/link to sequence file.
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59 if options.use_seq_data:
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60 if options.ref_file:
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61 # Sequence data from history.
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62 # Create symbolic link to ref_file so that index will be created in working directory.
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63 seq_path = "ref.fa"
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64 os.symlink(options.ref_file, seq_path)
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65 else:
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66 if not os.path.exists(options.index):
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67 stop_err('Reference genome %s not present, request it by reporting this error.' % options.index)
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68 seq_path = options.index
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69
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70 # Build command.
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71
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72 # Base.
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73 cmd = "cuffcompare -o cc_output "
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74
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75 # Add options.
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76 if options.ref_annotation:
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77 cmd += " -r %s " % options.ref_annotation
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78 if options.ignore_nonoverlap_reference:
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79 cmd += " -R "
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80 if options.ignore_nonoverlap_transfrag:
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81 cmd += " -Q "
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82 if options.use_seq_data:
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83 cmd += " -s %s " % seq_path
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84 if options.discard_single_exon_all:
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85 cmd += " -M "
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86 if options.discard_single_exon_ref:
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87 cmd += " -N "
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88 if options.max_dist_exon:
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89 cmd += " -e %i " % int(options.max_dist_exon)
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90 if options.max_dist_group:
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91 cmd += " -d %i " % int(options.max_dist_group)
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92 if options.discard_redundant_intron_transfrags:
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93 cmd += " -F "
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94 # Add input files.
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95
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96 # Need to symlink inputs so that output files are written to the current directory.
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97 for i, arg in enumerate(args):
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98 input_file_name = "./input%i" % (i + 1)
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99 os.symlink(arg, input_file_name)
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100 cmd += "%s " % input_file_name
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101
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102 # Run command.
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103 try:
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104 with tempfile.NamedTemporaryFile(dir=".") as tmp_stderr:
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105 returncode = subprocess.call(args=cmd, stderr=tmp_stderr, shell=True)
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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106
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107 # Error checking.
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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108 if returncode != 0:
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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109 # Get stderr, allowing for case where it's very large.
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110 buffsize = 1048576
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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111 stderr = ''
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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112 with open(tmp_stderr.name) as tmp_stderr2:
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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113 try:
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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114 while True:
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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115 stderr += tmp_stderr2.read(buffsize)
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 not stderr or len(stderr) % buffsize != 0:
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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117 break
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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118 except OverflowError:
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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119 pass
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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120 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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121
0
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122 # Copy outputs.
8
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123 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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124
0
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125 # check that there are results in the output file
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126 cc_output_fname = "cc_output.stats"
8
1322b73ffe44 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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127 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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128 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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129 except Exception as e:
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130 stop_err('Error running cuffcompare: %s' % e)
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131
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132
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133 if __name__ == "__main__":
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134 __main__()