Mercurial > repos > jjohnson > cummerbund

annotate cuffdiff_wrapper.py @ 11:56bdf6d4ac9c

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cuffdiff_wrapper.xml - allow either gtf of gff3 format for annotation input.
author Jim Johnson <jj@umn.edu>
date Fri, 19 Oct 2012 13:41:16 -0500
parents 6a9bc26ab8d9
children 4597c429b6fb
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1 #!/usr/bin/env python
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2
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3 # Wrapper supports Cuffdiff versions v1.3.0-v2.0
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4
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5 import optparse, os, shutil, subprocess, sys, tempfile
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6
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7 def group_callback( option, op_str, value, parser ):
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8 groups = []
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9 flist = []
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10 for arg in parser.rargs:
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11 arg = arg.strip()
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12 if arg[0] is "-":
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13 break
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14 elif arg[0] is ",":
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15 groups.append(flist)
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16 flist = []
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17 else:
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18 flist.append(arg)
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19 groups.append(flist)
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20
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21 setattr(parser.values, option.dest, groups)
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22
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23 def label_callback( option, op_str, value, parser ):
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24 labels = []
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25 for arg in parser.rargs:
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26 arg = arg.strip()
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27 if arg[0] is "-":
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28 break
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29 else:
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30 labels.append(arg)
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31
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32 setattr(parser.values, option.dest, labels)
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33
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34 def stop_err( msg ):
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35 sys.stderr.write( "%s\n" % msg )
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36 sys.exit()
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37
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38 # Copied from sam_to_bam.py:
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39 def check_seq_file( dbkey, cached_seqs_pointer_file ):
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40 seq_path = ''
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41 for line in open( cached_seqs_pointer_file ):
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42 line = line.rstrip( '\r\n' )
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43 if line and not line.startswith( '#' ) and line.startswith( 'index' ):
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44 fields = line.split( '\t' )
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45 if len( fields ) < 3:
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46 continue
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47 if fields[1] == dbkey:
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48 seq_path = fields[2].strip()
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49 break
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50 return seq_path
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51
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52 def __main__():
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53 #Parse Command Line
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54 parser = optparse.OptionParser()
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55
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56 # Cuffdiff options.
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57 parser.add_option( '-s', '--inner-dist-std-dev', dest='inner_dist_std_dev', help='The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp.' )
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58 parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' )
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59 parser.add_option( '-m', '--inner-mean-dist', dest='inner_mean_dist', help='This is the expected (mean) inner distance between mate pairs. \
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60 For, example, for paired end runs with fragments selected at 300bp, \
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61 where each end is 50bp, you should set -r to be 200. The default is 45bp.')
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62 parser.add_option( '-c', '--min-alignment-count', dest='min_alignment_count', help='The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not signficant, and the locus\' observed changes don\'t contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).' )
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63 parser.add_option( '--FDR', dest='FDR', help='The allowed false discovery rate. The default is 0.05.' )
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64 parser.add_option( '-u', '--multi-read-correct', dest='multi_read_correct', action="store_true", help='Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome')
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65
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66 # Advanced Options:
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67 parser.add_option( '--num-importance-samples', dest='num_importance_samples', help='Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000' )
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68 parser.add_option( '--max-mle-iterations', dest='max_mle_iterations', help='Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000' )
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69
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70 # Wrapper / Galaxy options.
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71 parser.add_option( '-f', '--files', dest='groups', action="callback", callback=group_callback, help="Groups to be processed, groups are separated by spaces, replicates in a group comma separated. group1_rep1,group1_rep2 group2_rep1,group2_rep2, ..., groupN_rep1, groupN_rep2" )
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72 parser.add_option( '-A', '--inputA', dest='inputA', help='A transcript GTF file produced by cufflinks, cuffcompare, or other source.')
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73 parser.add_option( '-1', '--input1', dest='input1', help='File of RNA-Seq read alignments in the SAM format. SAM is a standard short read alignment, that allows aligners to attach custom tags to individual alignments, and Cufflinks requires that the alignments you supply have some of these tags. Please see Input formats for more details.' )
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74 parser.add_option( '-2', '--input2', dest='input2', help='File of RNA-Seq read alignments in the SAM format. SAM is a standard short read alignment, that allows aligners to attach custom tags to individual alignments, and Cufflinks requires that the alignments you supply have some of these tags. Please see Input formats for more details.' )
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75
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76 # Label options
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77 parser.add_option('-L', '--labels', dest='labels', action="callback", callback=label_callback, help="Labels for the groups the replicates are in.")
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78
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79 # Normalization options.
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80 parser.add_option( "-N", "--quartile-normalization", dest="do_normalization", action="store_true" )
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81
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82 # Bias correction options.
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83 parser.add_option( '-b', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.')
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84 parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' )
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85 parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' )
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86 parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' )
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87
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88 # Outputs.
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89 parser.add_option( "--isoforms_fpkm_tracking_output", dest="isoforms_fpkm_tracking_output" )
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90 parser.add_option( "--genes_fpkm_tracking_output", dest="genes_fpkm_tracking_output" )
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91 parser.add_option( "--cds_fpkm_tracking_output", dest="cds_fpkm_tracking_output" )
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92 parser.add_option( "--tss_groups_fpkm_tracking_output", dest="tss_groups_fpkm_tracking_output" )
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93 parser.add_option( "--isoforms_read_group_tracking_output", dest="isoforms_read_group_tracking_output", default=None)
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94 parser.add_option( "--genes_read_group_tracking_output", dest="genes_read_group_tracking_output", default=None )
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95 parser.add_option( "--cds_read_group_tracking_output", dest="cds_read_group_tracking_output", default=None )
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96 parser.add_option( "--tss_groups_read_group_tracking_output", dest="tss_groups_read_group_tracking_output", default=None )
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97 parser.add_option( "--isoforms_exp_output", dest="isoforms_exp_output" )
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98 parser.add_option( "--genes_exp_output", dest="genes_exp_output" )
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99 parser.add_option( "--tss_groups_exp_output", dest="tss_groups_exp_output" )
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100 parser.add_option( "--cds_exp_fpkm_tracking_output", dest="cds_exp_fpkm_tracking_output" )
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101 parser.add_option( "--cds_diff_output", dest="cds_diff_output" )
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102 parser.add_option( "--isoforms_count_tracking_output", dest="isoforms_count_tracking_output" )
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103 parser.add_option( "--genes_count_tracking_output", dest="genes_count_tracking_output" )
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104 parser.add_option( "--cds_count_tracking_output", dest="cds_count_tracking_output" )
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105 parser.add_option( "--tss_groups_count_tracking_output", dest="tss_groups_count_tracking_output" )
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106 parser.add_option( "--splicing_diff_output", dest="splicing_diff_output" )
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107 parser.add_option( "--promoters_diff_output", dest="promoters_diff_output" )
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108 parser.add_option( "--run_info_output", dest="run_info_output" )
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109 parser.add_option( "--read_groups_info_output", dest="read_groups_info_output" )
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110 parser.add_option( "--cuffdatadir", dest="cuffdatadir", default=None)
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111 parser.add_option( "--cummeRbund_db_output", dest="cummeRbund_db_output", default=None)
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112
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diff changeset
113 (options, args) = parser.parse_args()
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
114
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
115 # output version # of tool
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
116 try:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
117 tmp = tempfile.NamedTemporaryFile().name
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
118 tmp_stdout = open( tmp, 'wb' )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
119 proc = subprocess.Popen( args='cuffdiff --no-update-check 2>&1', shell=True, stdout=tmp_stdout )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
120 tmp_stdout.close()
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
121 returncode = proc.wait()
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
122 stdout = None
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
123 for line in open( tmp_stdout.name, 'rb' ):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
124 if line.lower().find( 'cuffdiff v' ) >= 0:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
125 stdout = line.strip()
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
126 break
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
127 if stdout:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
128 sys.stdout.write( '%s\n' % stdout )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
129 else:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
130 raise Exception
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
131 except:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
132 sys.stdout.write( 'Could not determine Cuffdiff version\n' )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
133
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
134 # Make temp directory for output.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
135 tmp_output_dir = tempfile.mkdtemp()
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
136 cuffdatadir = options.cuffdatadir if options.cuffdatadir else tmp_output_dir
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
137 if not os.path.exists( cuffdatadir ):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
138 os.makedirs( cuffdatadir )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
139
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
140
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
141 # If doing bias correction, set/link to sequence file.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
142 if options.do_bias_correction:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
143 if options.ref_file != 'None':
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
144 # Sequence data from history.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
145 # Create symbolic link to ref_file so that index will be created in working directory.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
146 seq_path = os.path.join( cuffdatadir, "ref.fa" )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
147 os.symlink( options.ref_file, seq_path )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
148 else:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
149 # Sequence data from loc file.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
150 cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
151 if not os.path.exists( cached_seqs_pointer_file ):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
152 stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
153 # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa,
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
154 # and the equCab2.fa file will contain fasta sequences.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
155 seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
156 if seq_path == '':
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
157 stop_err( 'No sequence data found for dbkey %s, so bias correction cannot be used.' % options.dbkey )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
158
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
159 # Build command.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
160
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
161 # Base; always use quiet mode to avoid problems with storing log output.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
162 cmd = "cuffdiff --no-update-check -q"
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
163
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
164 # Add options.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
165 if options.inner_dist_std_dev:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
166 cmd += ( " -s %i" % int ( options.inner_dist_std_dev ) )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
167 if options.num_threads:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
168 cmd += ( " -p %i" % int ( options.num_threads ) )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
169 if options.inner_mean_dist:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
170 cmd += ( " -m %i" % int ( options.inner_mean_dist ) )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
171 if options.min_alignment_count:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
172 cmd += ( " -c %i" % int ( options.min_alignment_count ) )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
173 if options.FDR:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
174 cmd += ( " --FDR %f" % float( options.FDR ) )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
175 if options.multi_read_correct:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
176 cmd += ( " -u" )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
177 if options.num_importance_samples:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
178 cmd += ( " --num-importance-samples %i" % int ( options.num_importance_samples ) )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
179 if options.max_mle_iterations:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
180 cmd += ( " --max-mle-iterations %i" % int ( options.max_mle_iterations ) )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
181 if options.do_normalization:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
182 cmd += ( " -N" )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
183 if options.do_bias_correction:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
184 cmd += ( " -b %s" % seq_path )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
185
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
186 # Add inputs.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
187 # For replicate analysis: group1_rep1,group1_rep2 groupN_rep1,groupN_rep2
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
188 if options.groups:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
189 cmd += " --labels "
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
190 for label in options.labels:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
191 cmd += label + ","
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
192 cmd = cmd[:-1]
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
193
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
194 cmd += " " + options.inputA + " "
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
195
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
196 for group in options.groups:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
197 for filename in group:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
198 cmd += filename + ","
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
199 cmd = cmd[:-1] + " "
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
200 else:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
201 cmd += " " + options.inputA + " " + options.input1 + " " + options.input2
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
202
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
203 # Debugging.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
204 print cmd
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
205
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
206 # Run command.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
207 try:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
208 tmp_name = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
209 tmp_stderr = open( tmp_name, 'wb' )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
210 proc = subprocess.Popen( args=cmd, shell=True, cwd=cuffdatadir, stderr=tmp_stderr.fileno() )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
211 returncode = proc.wait()
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
212 tmp_stderr.close()
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
213
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
214 # Get stderr, allowing for case where it's very large.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
215 tmp_stderr = open( tmp_name, 'rb' )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
216 stderr = ''
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
217 buffsize = 1048576
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
218 try:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
219 while True:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
220 stderr += tmp_stderr.read( buffsize )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
221 if not stderr or len( stderr ) % buffsize != 0:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
222 break
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
223 except OverflowError:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
224 pass
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
225 tmp_stderr.close()
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
226
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
227 # Error checking.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
228 if returncode != 0:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
229 raise Exception, stderr
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
230
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
231 # check that there are results in the output file
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
232 if len( open( os.path.join( cuffdatadir, "isoforms.fpkm_tracking" ), 'rb' ).read().strip() ) == 0:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
233 raise Exception, 'The main output file is empty, there may be an error with your input file or settings.'
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
234 except Exception, e:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
235 stop_err( 'Error running cuffdiff. ' + str( e ) )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
236
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
237
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
238 # Copy output files from tmp directory to specified files.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
239 try:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
240 try:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
241 if options.isoforms_fpkm_tracking_output and os.path.exists(os.path.join( cuffdatadir, "isoforms.fpkm_tracking" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
242 shutil.copyfile( os.path.join( cuffdatadir, "isoforms.fpkm_tracking" ), options.isoforms_fpkm_tracking_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
243 if options.genes_fpkm_tracking_output and os.path.exists(os.path.join( cuffdatadir, "genes.fpkm_tracking" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
244 shutil.copyfile( os.path.join( cuffdatadir, "genes.fpkm_tracking" ), options.genes_fpkm_tracking_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
245 if options.cds_fpkm_tracking_output and os.path.exists(os.path.join( cuffdatadir, "cds.fpkm_tracking" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
246 shutil.copyfile( os.path.join( cuffdatadir, "cds.fpkm_tracking" ), options.cds_fpkm_tracking_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
247 if options.tss_groups_fpkm_tracking_output and os.path.exists(os.path.join( cuffdatadir, "tss_groups.fpkm_tracking" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
248 shutil.copyfile( os.path.join( cuffdatadir, "tss_groups.fpkm_tracking" ), options.tss_groups_fpkm_tracking_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
249
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
250 if options.isoforms_read_group_tracking_output and os.path.exists(os.path.join( cuffdatadir, "isoforms.read_group_tracking" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
251 shutil.copyfile( os.path.join( cuffdatadir, "isoforms.read_group_tracking" ), options.isoforms_read_group_tracking_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
252 if options.genes_read_group_tracking_output and os.path.exists(os.path.join( cuffdatadir, "genes.read_group_tracking" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
253 shutil.copyfile( os.path.join( cuffdatadir, "genes.read_group_tracking" ), options.genes_read_group_tracking_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
254 if options.cds_read_group_tracking_output and os.path.exists(os.path.join( cuffdatadir, "cds.read_group_tracking" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
255 shutil.copyfile( os.path.join( cuffdatadir, "cds.read_group_tracking" ), options.cds_read_group_tracking_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
256 if options.tss_groups_read_group_tracking_output and os.path.exists(os.path.join( cuffdatadir, "tss_groups.read_group_tracking" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
257 shutil.copyfile( os.path.join( cuffdatadir, "tss_groups.read_group_tracking" ), options.tss_groups_read_group_tracking_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
258
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
259 if options.isoforms_exp_output and os.path.exists(os.path.join( cuffdatadir, "isoform_exp.diff" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
260 shutil.copyfile( os.path.join( cuffdatadir, "isoform_exp.diff" ), options.isoforms_exp_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
261 if options.genes_exp_output and os.path.exists(os.path.join( cuffdatadir, "gene_exp.diff" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
262 shutil.copyfile( os.path.join( cuffdatadir, "gene_exp.diff" ), options.genes_exp_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
263 if options.cds_exp_fpkm_tracking_output and os.path.exists(os.path.join( cuffdatadir, "cds_exp.diff" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
264 shutil.copyfile( os.path.join( cuffdatadir, "cds_exp.diff" ), options.cds_exp_fpkm_tracking_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
265 if options.tss_groups_exp_output and os.path.exists(os.path.join( cuffdatadir, "tss_group_exp.diff" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
266 shutil.copyfile( os.path.join( cuffdatadir, "tss_group_exp.diff" ), options.tss_groups_exp_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
267
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
268 if options.isoforms_count_tracking_output and os.path.exists(os.path.join( cuffdatadir, "isoforms.count_tracking" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
269 shutil.copyfile( os.path.join( cuffdatadir, "isoforms.count_tracking" ), options.isoforms_count_tracking_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
270 if options.genes_count_tracking_output and os.path.exists(os.path.join( cuffdatadir, "genes.count_tracking" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
271 shutil.copyfile( os.path.join( cuffdatadir, "genes.count_tracking" ), options.genes_count_tracking_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
272 if options.cds_count_tracking_output and os.path.exists(os.path.join( cuffdatadir, "cds.count_tracking" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
273 shutil.copyfile( os.path.join( cuffdatadir, "cds.count_tracking" ), options.cds_count_tracking_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
274 if options.tss_groups_count_tracking_output and os.path.exists(os.path.join( cuffdatadir, "tss_groups.count_tracking" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
275 shutil.copyfile( os.path.join( cuffdatadir, "tss_groups.count_tracking" ), options.tss_groups_count_tracking_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
276
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
277 if options.cds_diff_output and os.path.exists(os.path.join( cuffdatadir, "cds.diff" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
278 shutil.copyfile( os.path.join( cuffdatadir, "cds.diff" ), options.cds_diff_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
279
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
280 if options.splicing_diff_output and os.path.exists(os.path.join( cuffdatadir, "splicing.diff" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
281 shutil.copyfile( os.path.join( cuffdatadir, "splicing.diff" ), options.splicing_diff_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
282 if options.promoters_diff_output and os.path.exists(os.path.join( cuffdatadir, "promoters.diff" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
283 shutil.copyfile( os.path.join( cuffdatadir, "promoters.diff" ), options.promoters_diff_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
284
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
285 if options.run_info_output and os.path.exists(os.path.join( cuffdatadir, "run.info" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
286 shutil.copyfile( os.path.join( cuffdatadir, "run.info" ), options.run_info_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
287 if options.read_groups_info_output and os.path.exists(os.path.join( cuffdatadir, "read_groups.info" )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
288 shutil.copyfile( os.path.join( cuffdatadir, "read_groups.info" ), options.read_groups_info_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
289
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
290 except Exception, e:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
291 stop_err( 'Error in cuffdiff:\n' + str( e ) )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
292 if options.cummeRbund_db_output:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
293 try:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
294 dbFile = 'cuffData.db'
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
295 rscript = tempfile.NamedTemporaryFile( dir=tmp_output_dir,suffix='.r' ).name
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
296 rscript_fh = open( rscript, 'wb' )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
297 rscript_fh.write('library(cummeRbund)\n')
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
298 if options.inputA and options.ref_file:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
299 rscript_fh.write('cuff<-readCufflinks(dir = "%s", dbFile = "%s", gtfFile = "%s", genome = "%s", rebuild = T)\n' % (cuffdatadir,dbFile,options.inputA,options.ref_file))
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
300 else:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
301 rscript_fh.write('cuff<-readCufflinks(dir = "%s", dbFile = "%s", rebuild = T)\n' % (cuffdatadir,dbFile))
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
302 rscript_fh.close()
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
303 cmd = ( "Rscript --vanilla %s" % rscript )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
304 tmp_name = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
305 tmp_stderr = open( tmp_name, 'wb' )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
306 proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
307 #proc = subprocess.Popen( args=cmd, shell=True)
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
308 returncode = proc.wait()
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
309 tmp_stderr.close()
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
310 if os.path.exists(os.path.join( cuffdatadir, dbFile )):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
311 shutil.copyfile( os.path.join( cuffdatadir, dbFile ), options.cummeRbund_db_output )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
312 shutil.rmtree(os.path.join( cuffdatadir, dbFile ))
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
313 except Exception, e:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
314 stop_err( 'Error generating cummeRbund cuffData.db:\n' + str( e ) )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
315 finally:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
316 # Clean up temp dirs
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
317 if os.path.exists( tmp_output_dir ):
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
318 shutil.rmtree( tmp_output_dir )
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
319
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
320 if __name__=="__main__": __main__()