Mercurial > repos > devteam > picard
diff picard_SamToFastq_wrapper.py @ 0:ff4ec13e496e draft
Uploaded tarball to repository
author | devteam |
---|---|
date | Tue, 23 Oct 2012 10:49:35 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_SamToFastq_wrapper.py Tue Oct 23 10:49:35 2012 -0400 @@ -0,0 +1,93 @@ +#!/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__()