--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_SamToFastq_wrapper.py	Tue Aug 13 12:09:14 2013 -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__()