Mercurial > repos > fubar > data_manager_rnasta
view data_manager/rnastar_index_builder.py @ 0:84f6e67cbae5 draft
Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
author | fubar |
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date | Mon, 29 Sep 2014 20:25:10 -0400 |
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children | ebadd2c92958 |
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#!/usr/bin/env python #Dan Blankenberg # adapted from Dan's BWA one for rna star # ross lazarus sept 2014 # import sys import os import tempfile import optparse import subprocess from galaxy.util.json import from_json_string, to_json_string DEFAULT_DATA_TABLE_NAME = "rnastar_indexes" def get_id_name( params, dbkey, fasta_description=None): #TODO: ensure sequence_id is unique and does not already appear in location file sequence_id = params['param_dict']['sequence_id'] if not sequence_id: sequence_id = dbkey sequence_name = params['param_dict']['sequence_name'] if not sequence_name: sequence_name = fasta_description if not sequence_name: sequence_name = dbkey return sequence_id, sequence_name def build_rnastar_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name, sjdbOverhang,sjdbGTFfile, sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript,sjdbGTFfeatureExon,sjdbGTFchrPrefix,n_threads): #TODO: allow multiple FASTA input files #tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-bwa-index-builder-' ) fasta_base_name = os.path.split( fasta_filename )[-1] sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) os.symlink( fasta_filename, sym_linked_fasta_filename ) pdict={'target_directory':target_directory,'n_threads':n_threads, 'sjdbFileChrStartEnd':sjdbFileChrStartEnd, 'sjdbGTFtagExonParentTranscript':sjdbGTFtagExonParentTranscript, 'sjdbGTFfeatureExon':sjdbGTFfeatureExon, 'sjdbGTFchrPrefix':sjdbGTFchrPrefix,'sjdbOverhang':sjdbOverhang, 'sjdbGTFfile':sjdbGTFfile, 'sym_linked_fasta_filename':sym_linked_fasta_filename} cl = 'STAR --runMode genomeGenerate --genomeFastaFiles %(sym_linked_fasta_filename)s --genomeDir %(target_directory)s --runThreadN %(n_threads)s' % pdict if sjdbGTFfile: cl += '''--sjdbGTFchrPrefix %(sjdbGTFchrPrefix)s --sjdbGTFfeatureExon %(sjdbGTFfeatureExon)s --sjdbOverhang %(sjdbOverhang)s --sjdbGTFfile %(sjdbGTFfile)s --sjdbGTFtagExonParentTranscript %(sjdbGTFtagExonParentTranscript)s''' % pdict elif sjdbFileChrStartEnd: cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s' tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar-index-builder-stderr" ) args = cl.split(' ') proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) return_code = proc.wait() if return_code: tmp_stderr.flush() tmp_stderr.seek(0) print >> sys.stderr, "Error building index: retcode=",retcode while True: chunk = tmp_stderr.read( CHUNK_SIZE ) if not chunk: break sys.stderr.write( chunk ) tmp_stderr.close() data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name ) _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) return data_manager_dict def main(): #Parse Command Line parser = optparse.OptionParser() parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' ) parser.add_option( '--out_file', default=None) parser.add_option( '--out_index_path', default=None) parser.add_option( '--sjdbGTFfile', type="string", default=None ) parser.add_option( '--sjdbGTFchrPrefix', type="string", default=None ) parser.add_option( '--sjdbGTFfeatureExon', type="string", default=None ) parser.add_option( '--sjdbGTFtagExonParentTranscript', type="string", default=None ) parser.add_option( '--sjdbFileChrStartEnd', type="string", default=None ) parser.add_option( '--sjdbOverhang', type="int", default=100 ) parser.add_option( '--runThreadN', type="int", default=4 ) (options, args) = parser.parse_args() filename = options.out_file params = from_json_string( open( filename ).read() ) target_directory = options.out_index_path os.mkdir( target_directory ) data_manager_dict = {} dbkey = options.fasta_dbkey if dbkey in [ None, '', '?' ]: raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) ) sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description ) #build the index build_rnastar_index( data_manager_dict, options.fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name, sjdbOverhang=options.sjdbOverhang,sjdbGTFfile=options.sjdbGTFfile, sjdbFileChrStartEnd=options.sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript=options.sjdbGTFtagExonParentTranscript, sjdbGTFfeatureExon=options.sjdbGTFfeatureExon,sjdbGTFchrPrefix=options.sjdbGTFchrPrefix, n_threads=options.runThreadN ) #save info to json file open( filename, 'wb' ).write( to_json_string( data_manager_dict ) ) if __name__ == "__main__": main()