#!/usr/bin/env python
#Dan Blankenberg
"""
A wrapper script for converting SAM to BAM, with sorting.
%prog input_filename.sam output_filename.bam
"""
import sys, optparse, os, tempfile, subprocess, shutil
CHUNK_SIZE = 2**20 #1mb
[docs]def cleanup_before_exit( tmp_dir ):
if tmp_dir and os.path.exists( tmp_dir ):
shutil.rmtree( tmp_dir )
def __main__():
#Parse Command Line
parser = optparse.OptionParser()
(options, args) = parser.parse_args()
assert len( args ) == 2, 'You must specify the input and output filenames'
input_filename, output_filename = args
tmp_dir = tempfile.mkdtemp( prefix='tmp-sam_to_bam_converter-' )
#convert to SAM
unsorted_bam_filename = os.path.join( tmp_dir, 'unsorted.bam' )
unsorted_stderr_filename = os.path.join( tmp_dir, 'unsorted.stderr' )
cmd = 'samtools view -bS "%s" > "%s"' % ( input_filename, unsorted_bam_filename )
proc = subprocess.Popen( args=cmd, stderr=open( unsorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir )
return_code = proc.wait()
if return_code:
stderr_target = sys.stderr
else:
stderr_target = sys.stdout
stderr = open( unsorted_stderr_filename )
while True:
chunk = stderr.read( CHUNK_SIZE )
if chunk:
stderr_target.write( chunk )
else:
break
stderr.close()
#sort sam, so indexing will not fail
sorted_stderr_filename = os.path.join( tmp_dir, 'sorted.stderr' )
sorting_prefix = os.path.join( tmp_dir, 'sorted_bam' )
cmd = 'samtools sort -o "%s" "%s" > "%s"' % ( unsorted_bam_filename, sorting_prefix, output_filename )
proc = subprocess.Popen( args=cmd, stderr=open( sorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir )
return_code = proc.wait()
if return_code:
stderr_target = sys.stderr
else:
stderr_target = sys.stdout
stderr = open( sorted_stderr_filename )
while True:
chunk = stderr.read( CHUNK_SIZE )
if chunk:
stderr_target.write( chunk )
else:
break
stderr.close()
cleanup_before_exit( tmp_dir )
if __name__=="__main__": __main__()