Mercurial > repos > devteam > data_manager_sam_fasta_index_builder
view data_manager/data_manager_sam_fasta_index_builder.py @ 1:cf875cbe2df4 draft
Uploaded updated data manager that specifies samtools 0.1.19.
author | devteam |
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date | Thu, 27 Mar 2014 15:08:42 -0400 |
parents | d6b6db69d9bf |
children | 2a1ac1abc3f7 |
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#!/usr/bin/env python #Dan Blankenberg import json import optparse import os import subprocess import sys import tempfile CHUNK_SIZE = 2**20 DEFAULT_DATA_TABLE_NAME = "fasta_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_sam_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ): #TODO: allow multiple FASTA input files 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 ) args = [ 'samtools', 'faidx' ] args.append( sym_linked_fasta_filename ) tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-sam_fa_index_builder-stderr" ) 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 ) sys.stderr.write( "Error building index:\n" ) while True: chunk = tmp_stderr.read( CHUNK_SIZE ) if not chunk: break sys.stderr.write( chunk ) sys.exit( return_code ) 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' ) (options, args) = parser.parse_args() filename = args[0] params = json.loads( open( filename ).read() ) target_directory = params[ 'output_data' ][0]['extra_files_path'] os.mkdir( target_directory ) data_manager_dict = {} if options.fasta_dbkey in [ None, '', '?' ]: raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) ) sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description ) #build the index build_sam_index( data_manager_dict, options.fasta_filename, target_directory, options.fasta_dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME ) #save info to json file open( filename, 'wb' ).write( json.dumps( data_manager_dict ) ) if __name__ == "__main__": main()