view data_manager/salmon_index_builder.py @ 4:566207ae614c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54

#!/usr/bin/env python
# Based heavily on the kallisto data manager wrapper script by iuc
from __future__ import print_function

import argparse
import json
import os
import subprocess
import sys

DEFAULT_DATA_TABLE_NAME = "salmon_indexes_versioned"


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_salmon_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)
    args = ['salmon', 'index']
    if options.kmer_size != '':
        args.append('-k')
        args.append(options.kmer_size)
    args.extend(['-t', options.fasta_filename, '-i', target_directory])
    return_code = subprocess.call(args=args, shell=False)
    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, version=options.index_version)
    _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='salmon_indexes')
    parser.add_argument('-v', '--index_version', dest='index_version', action='store', type=str, help='Use IndexVersion attribute from header.json')
    parser.add_argument('-k', '--kmer_size', dest='kmer_size', action='store', type=str, help='kmer_size')
    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_salmon_index(data_manager_dict, options, params, sequence_id, sequence_name)

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


if __name__ == "__main__":
    main()