Mercurial > repos > devteam > data_manager_gatk_picard_index_builder
view data_manager/data_manager_gatk_picard_index_builder.py @ 0:619dd9e9c09c draft
Imported from capsule None
author | devteam |
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date | Tue, 01 Apr 2014 10:48:03 -0400 |
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children | b31f1fcb203c |
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#!/usr/bin/env python # Dave B. # Uses fasta sorting functions written by Dan Blankenberg. import json import optparse import os import shutil 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_picard_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, jar, data_table_name=DEFAULT_DATA_TABLE_NAME ): fasta_base_name = os.path.split( fasta_filename )[-1] gatk_sorted_fasta_filename = os.path.join( target_directory, fasta_base_name ) shutil.copy( fasta_filename, gatk_sorted_fasta_filename ) _sort_fasta_gatk( gatk_sorted_fasta_filename ) sam_index_filename = '%s.fai' % gatk_sorted_fasta_filename if not os.path.exists( sam_index_filename ): sam_command = [ 'samtools', 'faidx', gatk_sorted_fasta_filename ] _run_command( sam_command, target_directory ) args = [ 'java', '-jar', jar, 'R=%s' % gatk_sorted_fasta_filename, 'O=%s.dict' % sequence_id ] _run_command( args, target_directory ) 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 _run_command( command, target_directory ): tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-gatk_picard_index_builder-stderr" ) proc = subprocess.Popen( args=command, 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() 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 _move_and_index_fasta_for_sorting( fasta_filename ): unsorted_filename = tempfile.NamedTemporaryFile().name shutil.move( fasta_filename, unsorted_filename ) fasta_offsets = {} unsorted_fh = open( unsorted_filename ) while True: offset = unsorted_fh.tell() line = unsorted_fh.readline() if not line: break if line.startswith( ">" ): line = line.split( None, 1 )[0][1:] fasta_offsets[ line ] = offset unsorted_fh.close() current_order = map( lambda x: x[1], sorted( map( lambda x: ( x[1], x[0] ), fasta_offsets.items() ) ) ) return ( unsorted_filename, fasta_offsets, current_order ) def _write_sorted_fasta( sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename ): unsorted_fh = open( unsorted_fasta_filename ) sorted_fh = open( sorted_fasta_filename, 'wb+' ) for name in sorted_names: offset = fasta_offsets[ name ] unsorted_fh.seek( offset ) sorted_fh.write( unsorted_fh.readline() ) while True: line = unsorted_fh.readline() if not line or line.startswith( ">" ): break sorted_fh.write( line ) unsorted_fh.close() sorted_fh.close() def _int_to_roman( integer ): if not isinstance( integer, int ): raise TypeError, "expected integer, got %s" % type( integer ) if not 0 < integer < 4000: raise ValueError, "Argument must be between 1 and 3999, got %s" % str( integer ) ints = ( 1000, 900, 500, 400, 100, 90, 50, 40, 10, 9, 5, 4, 1 ) nums = ( 'M', 'CM', 'D', 'CD', 'C', 'XC', 'L', 'XL', 'X', 'IX', 'V', 'IV', 'I' ) result = "" for i in range( len( ints ) ): count = int( integer / ints[ i ] ) result += nums[ i ] * count integer -= ints[ i ] * count return result def _sort_fasta_gatk( fasta_filename ): ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename ) sorted_names = map( str, range( 1, 100 ) ) + map( _int_to_roman, range( 1, 100 ) ) + [ 'X', 'Y', 'M' ] #detect if we have chrN, or just N has_chr = False for chrom in sorted_names: if "chr%s" % chrom in current_order: has_chr = True break if has_chr: sorted_names = map( lambda x: "chr%s" % x, sorted_names) else: sorted_names.insert( 0, "MT" ) sorted_names.extend( map( lambda x: "%s_random" % x, sorted_names ) ) existing_sorted_names = [] for name in sorted_names: # Append each chromosome only once. if name in current_order and name not in existing_sorted_names: existing_sorted_names.append( name ) for name in current_order: #TODO: confirm that non-canonical names do not need to be sorted specially if name not in existing_sorted_names: existing_sorted_names.append( name ) if existing_sorted_names == current_order: shutil.move( unsorted_filename, fasta_filename ) else: _write_sorted_fasta( existing_sorted_names, fasta_offsets, fasta_filename, unsorted_filename ) 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( '-j', '--jar', dest='jar', action='store', type="string", default=None, help='GATK .jar file' ) (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_picard_index( data_manager_dict, options.fasta_filename, target_directory, options.fasta_dbkey, sequence_id, sequence_name, options.jar, 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()