comparison bismark_wrapper.py @ 20:0895fe70075d draft

Uploaded

19:30caca800c9b

    sys.stderr.write( "%s\n" % msg )
    sys.exit()

def __main__():

    #Parse Command Line
    parser = argparse.ArgumentParser(description='Wrapper for the bismark bisulfite mapper.')
    parser.add_argument( '-p', '--num-threads', dest='num_threads',
        type=int, default=4, help='Use this many threads to align reads. The default is 4.' )

    arguments.update( {'args': additional_opts, 'reads': reads} )

    # Final bismark command:
    cmd = cmd % arguments
    # Run
    try:
        tmp_out = tempfile.NamedTemporaryFile().name
        tmp_stdout = open( tmp_out, 'wb' )
        tmp_err = tempfile.NamedTemporaryFile().name

        """
            merge all bam files
        """
        #tmp_out = tempfile.NamedTemporaryFile( dir=output_dir ).name
        tmp_stdout = open( tmp_out, 'wab' )
        #tmp_err = tempfile.NamedTemporaryFile( dir=output_dir ).name
        tmp_stderr = open( tmp_err, 'wab' )

        tmp_res = tempfile.NamedTemporaryFile( dir= output_dir).name

        bam_files = glob( os.path.join( output_dir, '*.bam') )
        if len( bam_files ) > 1:

            tmp_stdout.close()
            tmp_stderr.close()
            if returncode != 0:
                raise Exception, open( tmp_stderr.name ).read()
        else:
            tmp_res = bam_files[0]

        bam_path = "%s" % tmp_res

        if os.path.exists( bam_path ):
            if args.sort_bam:
                cmd = 'samtools sort -@ %s %s sorted_bam' % (args.num_threads, bam_path)
                proc = subprocess.Popen( args=shlex.split( cmd ) )
                returncode = proc.wait()
                if returncode != 0:
                    raise Exception("Error during '%s'" % cmd)
                shutil.move( 'sorted_bam.bam', args.output )
            else:
                shutil.move( bam_path, args.output )
        else:
            stop_err( 'BAM file no found:\n' + str( bam_path ) )


    # TODO: look for errors in program output.
    except Exception, e:
        stop_err( 'Error in merging bam files:\n' + str( e ) )

20:0895fe70075d

    sys.stderr.write( "%s\n" % msg )
    sys.exit()

def __main__():

    print 'tempfile_location',tempfile.gettempdir()
    #Parse Command Line
    parser = argparse.ArgumentParser(description='Wrapper for the bismark bisulfite mapper.')
    parser.add_argument( '-p', '--num-threads', dest='num_threads',
        type=int, default=4, help='Use this many threads to align reads. The default is 4.' )

    arguments.update( {'args': additional_opts, 'reads': reads} )

    # Final bismark command:
    cmd = cmd % arguments
    print 'bismark_cmd:', cmd
    #sys.stderr.write( cmd )
    #sys.exit(1)
    # Run
    try:
        tmp_out = tempfile.NamedTemporaryFile().name
        tmp_stdout = open( tmp_out, 'wb' )
        tmp_err = tempfile.NamedTemporaryFile().name

        """
            merge all bam files
        """
        #tmp_out = tempfile.NamedTemporaryFile( dir=output_dir ).name
        tmp_stdout = open( tmp_out, 'wab' )
        tmp_err = tempfile.NamedTemporaryFile( dir=output_dir ).name
        tmp_stderr = open( tmp_err, 'wb' )

        tmp_res = tempfile.NamedTemporaryFile( dir= output_dir).name

        bam_files = glob( os.path.join( output_dir, '*.bam') )
        if len( bam_files ) > 1:

            tmp_stdout.close()
            tmp_stderr.close()
            if returncode != 0:
                raise Exception, open( tmp_stderr.name ).read()
        else:
	    tmp_res = bam_files[0]

        bam_path = "%s" % tmp_res

        if os.path.exists( bam_path ):
	    if args.sort_bam:
                cmd = 'samtools sort -@ %s %s %s' % (args.num_threads, bam_path, args.output) 
	    else:
                shutil.copy( bam_path, args.output )
        else:
            stop_err( 'BAM file no found:\n' + str( bam_path ) )
		


    # TODO: look for errors in program output.
    except Exception, e:
        stop_err( 'Error in merging bam files:\n' + str( e ) )