hisat2_index_builder.py

#!/usr/bin/env python
# Based heavily on the Bowtie 2 data manager wrapper script by Dan Blankenberg
from __future__ import print_function

import argparse
import json
import os
import shlex
import subprocess
import sys

DEFAULT_DATA_TABLE_NAME = "hisat2_indexes"


def get_id_name(params, dbkey, fasta_description=None):
    # TODO: ensure sequence_id is unique and does not already appear in location file
    sequence_id = params['param_dict']['sequence_id']
    if not sequence_id:
        sequence_id = dbkey

    sequence_name = params['param_dict']['sequence_name']
    if not sequence_name:
        sequence_name = fasta_description
        if not sequence_name:
            sequence_name = dbkey
    return sequence_id, sequence_name


def build_hisat_index(data_manager_dict, options, params, sequence_id, sequence_name):
    data_table_name = options.data_table_name or DEFAULT_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.split(options.fasta_filename)[-1]
    sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
    os.symlink(options.fasta_filename, sym_linked_fasta_filename)
    args = ['hisat2-build']
    args.extend(shlex.split(options.indexer_options))
    args.extend([sym_linked_fasta_filename, sequence_id])
    proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
    return_code = proc.wait()
    if return_code:
        print("Error building index.", file=sys.stderr)
        sys.exit(return_code)
    data_table_entry = dict(value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id)
    _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)


def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
    data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
    data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
    return data_manager_dict


def main():
    # Parse Command Line
    parser = argparse.ArgumentParser()
    parser.add_argument('--output', dest='output', action='store', type=str, default=None)
    parser.add_argument('--fasta_filename', dest='fasta_filename', action='store', type=str, default=None)
    parser.add_argument('--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None)
    parser.add_argument('--fasta_description', dest='fasta_description', action='store', type=str, default=None)
    parser.add_argument('--data_table_name', dest='data_table_name', action='store', type=str, default='hisat2_indexes')
    parser.add_argument('--indexer_options', dest='indexer_options', action='store', type=str, default='')
    options = parser.parse_args()

    filename = options.output

    with open(filename) as fh:
        params = json.load(fh)
    data_manager_dict = {}

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

    sequence_id, sequence_name = get_id_name(params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description)

    # build the index
    build_hisat_index(data_manager_dict, options, params, sequence_id, sequence_name)

    # save info to json file
    with open(filename, 'w') as fh:
        json.dump(data_manager_dict, fh, sort_keys=True)


if __name__ == "__main__":
    main()