Mercurial > repos > fubar > data_manager_rnasta

comparison data_manager/rnastar_index_builder.py @ 8:363d6797d366 draft default tip

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author fubar
date Fri, 09 Jan 2015 23:40:09 -0500
parents 5c7efaab6713
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7:5c7efaab6713 8:363d6797d366
73 break 73 break
74 sys.stderr.write( chunk ) 74 sys.stderr.write( chunk )
75 sys.exit( return_code ) 75 sys.exit( return_code )
76 tmp_stderr.close() 76 tmp_stderr.close()
77 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name ) 77 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
78 data_manager_dict = {}
79 data_manager_dict = _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) 78 data_manager_dict = _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
80 return data_manager_dict 79 return data_manager_dict
81 80
82 81
83 def main(): 82 def main():
107 try: 106 try:
108 os.mkdir( target_directory ) 107 os.mkdir( target_directory )
109 except OSError: 108 except OSError:
110 pass 109 pass
111 #build the index 110 #build the index
112 data_manager_dict = build_rnastar_index( data_manager_dict = data_manager_dict, fasta_filename = options.fasta_filename, target_directory = target_directory, 111 data_manager_dict = build_rnastar_index( data_manager_dict = {}, fasta_filename = options.fasta_filename, target_directory = target_directory,
113 dbkey = dbkey, sequence_id = sequence_id, sequence_name = sequence_name, data_table_name=options.data_table_name, 112 dbkey = dbkey, sequence_id = sequence_id, sequence_name = sequence_name, data_table_name=options.data_table_name,
114 sjdbOverhang=options.sjdbOverhang,sjdbGTFfile=options.sjdbGTFfile, 113 sjdbOverhang=options.sjdbOverhang,sjdbGTFfile=options.sjdbGTFfile,
115 sjdbFileChrStartEnd=options.sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript=options.sjdbGTFtagExonParentTranscript, 114 sjdbFileChrStartEnd=options.sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript=options.sjdbGTFtagExonParentTranscript,
116 sjdbGTFfeatureExon=options.sjdbGTFfeatureExon,sjdbGTFchrPrefix=options.sjdbGTFchrPrefix, 115 sjdbGTFfeatureExon=options.sjdbGTFfeatureExon,sjdbGTFchrPrefix=options.sjdbGTFchrPrefix,
117 n_threads=options.runThreadN ) 116 n_threads=options.runThreadN )