comparison bismark_wrapper.py @ 4:427fb56f2e41 draft default tip

- new options - fixes

3:7eefe5d6eecd

        if args.bowtie2:
            cmd_index = 'bismark_genome_preparation --bowtie2 %s ' % ( tmp_index_dir )
        else:
            cmd_index = 'bismark_genome_preparation %s ' % ( tmp_index_dir )
        if args.bismark_path:
            # add the path to the bismark perl scripts, that is needed for galaxy
            cmd_index = '%s/%s' % (args.bismark_path, cmd_index)
        try:
            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
            tmp_stderr = open( tmp, 'wb' )
            proc = subprocess.Popen( args=cmd_index, shell=True, cwd=tmp_index_dir, stdout=open(os.devnull, 'wb'), stderr=tmp_stderr.fileno() )
            returncode = proc.wait()

            if os.path.exists( tmp_index_dir ):
                shutil.rmtree( tmp_index_dir )
            stop_err( 'Error indexing reference sequence\n' + str( e ) )
        index_dir = tmp_index_dir
    else:
        index_dir = args.index_path

    # Build bismark command
    tmp_bismark_dir = tempfile.mkdtemp()
    output_dir = os.path.join( tmp_bismark_dir, 'results')
    cmd = 'bismark %(args)s --temp_dir %(tmp_bismark_dir)s -o %(output_dir)s --quiet %(genome_folder)s %(reads)s'
    if args.bismark_path:
        # add the path to the bismark perl scripts, that is needed for galaxy
        cmd = '%s/%s' % (args.bismark_path, cmd)

    arguments = {
        'genome_folder': index_dir,
        'args': '',
        'tmp_bismark_dir': tmp_bismark_dir,

        reads = ' %s ' % ( args.single_paired )


    if not args.bowtie2:
        # use bowtie specific options
        additional_opts += ' --best '
        if args.seed_mismatches:
            # --seedmms
            additional_opts += ' -n %s ' % args.seed_mismatches
        if args.seed_len:
            # --seedlen

4:427fb56f2e41

        if args.bowtie2:
            cmd_index = 'bismark_genome_preparation --bowtie2 %s ' % ( tmp_index_dir )
        else:
            cmd_index = 'bismark_genome_preparation %s ' % ( tmp_index_dir )
        if args.bismark_path:
            if os.path.exists(args.bismark_path):
                # add the path to the bismark perl scripts, that is needed for galaxy
                cmd_index = os.path.join(args.bismark_path, cmd_index)
            else:
                # assume the same directory as that script
                cmd_index = 'perl %s' % os.path.join(os.path.realpath(os.path.dirname(__file__)), cmd_index)
        try:
            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
            tmp_stderr = open( tmp, 'wb' )
            proc = subprocess.Popen( args=cmd_index, shell=True, cwd=tmp_index_dir, stdout=open(os.devnull, 'wb'), stderr=tmp_stderr.fileno() )
            returncode = proc.wait()

            if os.path.exists( tmp_index_dir ):
                shutil.rmtree( tmp_index_dir )
            stop_err( 'Error indexing reference sequence\n' + str( e ) )
        index_dir = tmp_index_dir
    else:
        # bowtie path is the path to the index directory and the first path of the index file name
        index_dir = os.path.dirname( args.index_path )

    # Build bismark command
    tmp_bismark_dir = tempfile.mkdtemp()
    output_dir = os.path.join( tmp_bismark_dir, 'results')
    cmd = 'bismark %(args)s --temp_dir %(tmp_bismark_dir)s -o %(output_dir)s --quiet %(genome_folder)s %(reads)s'

    if args.fasta:
        # he query input files (specified as mate1,mate2 or singles) are FastA
        cmd = '%s %s' % (cmd, '--fasta')
    elif args.fastq:
        cmd = '%s %s' % (cmd, '--fastq')

    if args.bismark_path:
        # add the path to the bismark perl scripts, that is needed for galaxy
        if os.path.exists(args.bismark_path):
            cmd = os.path.join(args.bismark_path, cmd)
        else:
            # assume the same directory as that script
            cmd = 'perl %s' % os.path.join(os.path.realpath(os.path.dirname(__file__)), cmd)

    arguments = {
        'genome_folder': index_dir,
        'args': '',
        'tmp_bismark_dir': tmp_bismark_dir,

        reads = ' %s ' % ( args.single_paired )


    if not args.bowtie2:
        # use bowtie specific options
        #additional_opts += ' --best ' # bug in bismark, --best is not available as option. Only --non-best, best-mode is activated by default
        if args.seed_mismatches:
            # --seedmms
            additional_opts += ' -n %s ' % args.seed_mismatches
        if args.seed_len:
            # --seedlen