comparison data_manager/bwameth_index_builder.py @ 1:f5a15a12a4c9 draft default tip

Uploaded

0:a801458261bb

from json import dumps, loads

DEFAULT_DATA_TABLE_NAME = "bwameth_indexes"


def build_hisat_index(data_manager_dict, params, args):
    data_table_name = args.data_table_name
    target_directory = params[ 'output_data' ][0]['extra_files_path']
    if not os.path.exists( target_directory ):
        os.mkdir( target_directory )
    fasta_base_name = os.path.basename(args.fasta_filename)
    sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
    os.symlink(options.fasta_filename, sym_linked_fasta_filename)
    args = ['bwameth.py', 'index', sym_linked_fasta_filename]
    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
    return_code = proc.wait()
    if return_code:
        print >> sys.stderr, "Error building index."

    if args.dbkey in [ None, '', '?' ]:
        raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (args.dbkey))

    # build the index
    build_hisat_index(data_manager_dict, args)

    # save info to json file
    open(filename, 'wb').write(dumps(data_manager_dict))

if __name__ == "__main__":

1:f5a15a12a4c9

from json import dumps, loads

DEFAULT_DATA_TABLE_NAME = "bwameth_indexes"


def build_bwameth_index(data_manager_dict, params, args):
    data_table_name = args.data_table_name
    target_directory = params[ 'output_data' ][0]['extra_files_path']
    if not os.path.exists( target_directory ):
        os.mkdir( target_directory )
    fasta_base_name = os.path.basename(args.fasta_filename)
    sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
    os.symlink(args.fasta_filename, sym_linked_fasta_filename)
    args = ['bwameth.py', 'index', sym_linked_fasta_filename]
    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
    return_code = proc.wait()
    if return_code:
        print >> sys.stderr, "Error building index."

    if args.dbkey in [ None, '', '?' ]:
        raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (args.dbkey))

    # build the index
    build_bwameth_index(data_manager_dict, params, args)

    # save info to json file
    open(filename, 'wb').write(dumps(data_manager_dict))

if __name__ == "__main__":