Mercurial > repos > fubar > data_manager_rnasta

comparison data_manager/rnastar_index_builder.py @ 1:ebadd2c92958 draft

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Uploaded
author fubar
date Mon, 29 Sep 2014 20:47:45 -0400
parents 84f6e67cbae5
children 8a2d16bfdae2
comparison
equal deleted inserted replaced
0:84f6e67cbae5 1:ebadd2c92958
41 cl = 'STAR --runMode genomeGenerate --genomeFastaFiles %(sym_linked_fasta_filename)s --genomeDir %(target_directory)s --runThreadN %(n_threads)s' % pdict 41 cl = 'STAR --runMode genomeGenerate --genomeFastaFiles %(sym_linked_fasta_filename)s --genomeDir %(target_directory)s --runThreadN %(n_threads)s' % pdict
42 if sjdbGTFfile: 42 if sjdbGTFfile:
43 cl += '''--sjdbGTFchrPrefix %(sjdbGTFchrPrefix)s --sjdbGTFfeatureExon %(sjdbGTFfeatureExon)s --sjdbOverhang %(sjdbOverhang)s 43 cl += '''--sjdbGTFchrPrefix %(sjdbGTFchrPrefix)s --sjdbGTFfeatureExon %(sjdbGTFfeatureExon)s --sjdbOverhang %(sjdbOverhang)s
44 --sjdbGTFfile %(sjdbGTFfile)s --sjdbGTFtagExonParentTranscript %(sjdbGTFtagExonParentTranscript)s''' % pdict 44 --sjdbGTFfile %(sjdbGTFfile)s --sjdbGTFtagExonParentTranscript %(sjdbGTFtagExonParentTranscript)s''' % pdict
45 elif sjdbFileChrStartEnd: 45 elif sjdbFileChrStartEnd:
46 cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s' 46 cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s' % pdict
47 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar-index-builder-stderr" ) 47 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar-index-builder-stderr" )
48 args = cl.split(' ') 48 args = cl.split(' ')
49 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) 49 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
50 return_code = proc.wait() 50 return_code = proc.wait()
51 if return_code: 51 if return_code:
102 build_rnastar_index( data_manager_dict, options.fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name, 102 build_rnastar_index( data_manager_dict, options.fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name,
103 sjdbOverhang=options.sjdbOverhang,sjdbGTFfile=options.sjdbGTFfile, 103 sjdbOverhang=options.sjdbOverhang,sjdbGTFfile=options.sjdbGTFfile,
104 sjdbFileChrStartEnd=options.sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript=options.sjdbGTFtagExonParentTranscript, 104 sjdbFileChrStartEnd=options.sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript=options.sjdbGTFtagExonParentTranscript,
105 sjdbGTFfeatureExon=options.sjdbGTFfeatureExon,sjdbGTFchrPrefix=options.sjdbGTFchrPrefix, 105 sjdbGTFfeatureExon=options.sjdbGTFfeatureExon,sjdbGTFchrPrefix=options.sjdbGTFchrPrefix,
106 n_threads=options.runThreadN ) 106 n_threads=options.runThreadN )
107
107 108
108 #save info to json file 109 #save info to json file
109 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) ) 110 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
110 111
111 if __name__ == "__main__": main() 112 if __name__ == "__main__": main()