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annotate cuffmerge_wrapper.py @ 12:1707a530e598 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author devteam
date Tue, 07 Feb 2017 18:39:42 -0500
parents b6e3849293b1
children cf747d1bd79a
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1 #!/usr/bin/env python
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2
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3 import optparse
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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4 import os
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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5 import shutil
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6 import subprocess
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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7 import sys
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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8 import tempfile
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10
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11 def stop_err(msg):
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12 sys.stderr.write('%s\n' % msg)
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13 sys.exit()
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16 def __main__():
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17 parser = optparse.OptionParser()
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18 parser.add_option('-g', 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.')
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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19 parser.add_option('-s', dest='use_seq_data', action="store_true", help='Causes cuffmerge 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.')
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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20 parser.add_option('-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.')
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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21
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22 # Wrapper / Galaxy options.
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23 parser.add_option('', '--index', dest='index', help='The path of the reference genome')
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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24 parser.add_option('', '--ref_file', dest='ref_file', help='The reference dataset from the history')
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25
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26 # Outputs.
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27 parser.add_option('', '--merged-transcripts', dest='merged_transcripts')
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28 parser.add_option('--min-isoform-fraction', dest='min_isoform_fraction')
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29
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30 (options, args) = parser.parse_args()
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31
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32 # output version # of tool
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33 try:
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34 with tempfile.NamedTemporaryFile() as tmp_stdout:
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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35 returncode = subprocess.call(args='cuffmerge -v 2>&1', stdout=tmp_stdout, shell=True)
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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36 stdout = None
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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37 with open(tmp_stdout.name) as tmp_stdout2:
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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38 for line in tmp_stdout2:
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39 if line.lower().find('merge_cuff_asms v') >= 0:
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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40 stdout = line.strip()
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41 break
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42 if stdout:
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43 sys.stdout.write('%s\n' % stdout)
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44 else:
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45 raise Exception
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46 except:
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47 sys.stdout.write('Could not determine Cuffmerge version\n')
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48
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49 # Set/link to sequence file.
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50 if options.use_seq_data:
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51 if options.ref_file:
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52 # Sequence data from history.
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53 # Create symbolic link to ref_file so that index will be created in working directory.
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54 seq_path = "ref.fa"
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55 os.symlink(options.ref_file, seq_path)
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56 else:
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57 if not os.path.exists(options.index):
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58 stop_err('Reference genome %s not present, request it by reporting this error.' % options.index)
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59 seq_path = options.index
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60
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61 # Build command.
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62
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63 # Base.
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64 cmd = "cuffmerge -o cm_output "
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65
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66 # Add options.
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67 if options.num_threads:
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68 cmd += (" -p %i " % int(options.num_threads))
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69 if options.ref_annotation:
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70 cmd += " -g %s " % options.ref_annotation
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71 if options.use_seq_data:
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72 cmd += " -s %s " % seq_path
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73 if options.min_isoform_fraction:
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74 cmd += " --min-isoform-fraction %s " % (options.min_isoform_fraction)
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75 # Add input files to a file.
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76 with tempfile.NamedTemporaryFile(mode='w', dir=".", delete=False) as inputs_file:
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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77 for arg in args:
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78 inputs_file.write(arg + "\n")
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79 cmd += inputs_file.name
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80
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81 # Run command.
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82 try:
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83 with tempfile.NamedTemporaryFile(dir=".") as tmp_stderr:
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84 returncode = subprocess.call(args=cmd, stderr=tmp_stderr, shell=True)
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85
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86 # Error checking.
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87 if returncode != 0:
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88 # Get stderr, allowing for case where it's very large.
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89 buffsize = 1048576
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90 stderr = ''
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91 with open(tmp_stderr.name, 'r') as tmp_stderr2:
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92 try:
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93 while True:
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94 stderr += tmp_stderr2.read(buffsize)
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95 if not stderr or len(stderr) % buffsize != 0:
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96 break
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97 except OverflowError:
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98 pass
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99 raise Exception(stderr)
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100
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101 if len(open("cm_output/merged.gtf", 'r').read().strip()) == 0:
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102 raise Exception('The output file is empty, there may be an error with your input file or settings.')
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103
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104 # Copy outputs.
12
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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105 shutil.move("cm_output/merged.gtf", options.merged_transcripts)
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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parents: 10
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106 except Exception as e:
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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107 stop_err('Error running cuffmerge: %s' % e)
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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parents: 10
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108
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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109
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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110 if __name__ == "__main__":
1707a530e598 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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111 __main__()