Mercurial > repos > devteam > picard1106
view picard_SamToFastq_wrapper.py @ 144:db8e6c53acf5 draft
test please ignore
author | rayan |
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date | Mon, 16 Jun 2014 18:06:39 -0400 |
parents | 3321bce585e5 |
children |
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#!/usr/bin/env python #Dan Blankenberg """ A wrapper script for running the Picard SamToFastq command. Allows parsing read groups into separate files. """ import sys, optparse, os, tempfile, subprocess, shutil CHUNK_SIZE = 2**20 #1mb def cleanup_before_exit( tmp_dir ): if tmp_dir and os.path.exists( tmp_dir ): shutil.rmtree( tmp_dir ) def open_file_from_option( filename, mode = 'rb' ): if filename: return open( filename, mode = mode ) return None def __main__(): #Parse Command Line parser = optparse.OptionParser() parser.add_option( '-p', '--pass_through', dest='pass_through_options', action='append', type="string", help='These options are passed through directly to PICARD, without any modification.' ) parser.add_option( '-1', '--read_group_file_1', dest='read_group_file_1', action='store', type="string", default=None, help='Read Group 1 output file, when using multiple readgroups' ) parser.add_option( '-2', '--read_group_file_2', dest='read_group_file_2', action='store', type="string", default=None, help='Read Group 2 output file, when using multiple readgroups and paired end' ) parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' ) parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' ) parser.add_option( '-n', '--new_files_path', dest='new_files_path', action='store', type="string", default=None, help='new_files_path') parser.add_option( '-i', '--file_id_1', dest='file_id_1', action='store', type="string", default=None, help='file_id_1') parser.add_option( '-f', '--file_id_2', dest='file_id_2', action='store', type="string", default=None, help='file_id_2') (options, args) = parser.parse_args() tmp_dir = tempfile.mkdtemp( prefix='tmp-picard-' ) if options.pass_through_options: cmd = ' '.join( options.pass_through_options ) else: cmd = '' if options.new_files_path is not None: print 'Creating FASTQ files by Read Group' assert None not in [ options.read_group_file_1, options.new_files_path, options.file_id_1 ], 'When using read group aware, you need to specify --read_group_file_1, --read_group_file_2 (when paired end), --new_files_path, and --file_id' cmd = '%s OUTPUT_DIR="%s"' % ( cmd, tmp_dir) #set up stdout and stderr output options stdout = open_file_from_option( options.stdout, mode = 'wb' ) if stdout is None: stdout = sys.stdout stderr = open_file_from_option( options.stderr, mode = 'wb' ) #if no stderr file is specified, we'll use our own if stderr is None: stderr = tempfile.NamedTemporaryFile( prefix="picard-stderr-", dir=tmp_dir ) proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir ) return_code = proc.wait() if return_code: stderr_target = sys.stderr else: stderr_target = sys.stdout stderr.flush() stderr.seek(0) while True: chunk = stderr.read( CHUNK_SIZE ) if chunk: stderr_target.write( chunk ) else: break stderr.close() #if rg aware, put files where they belong if options.new_files_path is not None: fastq_1_name = options.read_group_file_1 fastq_2_name = options.read_group_file_2 file_id_1 = options.file_id_1 file_id_2 = options.file_id_2 if file_id_2 is None: file_id_2 = file_id_1 for filename in sorted( os.listdir( tmp_dir ) ): if filename.endswith( '_1.fastq' ): if fastq_1_name: shutil.move( os.path.join( tmp_dir, filename ), fastq_1_name ) fastq_1_name = None else: shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 1_visible_fastqsanger' % ( file_id_1, filename[:-len( '_1.fastq' )] ) ) ) elif filename.endswith( '_2.fastq' ): if fastq_2_name: shutil.move( os.path.join( tmp_dir, filename ), fastq_2_name ) fastq_2_name = None else: shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 2_visible_fastqsanger' % ( file_id_2, filename[:-len( '_2.fastq' )] ) ) ) cleanup_before_exit( tmp_dir ) if __name__=="__main__": __main__()