comparison data_manager/picard_index_builder.py @ 6:fa8c605bf385 draft default tip

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

5:acaa6719a478

#!/usr/bin/env python
# Dan Blankenberg
from __future__ import print_function

import optparse
import os
import subprocess
import sys
from json import dumps, loads

DEFAULT_DATA_TABLE_NAME = "picard_indexes"


def get_id_name(params, dbkey, fasta_description=None):

    parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name')
    (options, args) = parser.parse_args()

    filename = args[0]

    params = loads(open(filename).read())
    target_directory = params['output_data'][0]['extra_files_path']
    os.mkdir(target_directory)
    data_manager_dict = {}

    dbkey = options.fasta_dbkey

    # build the index
    build_picard_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id,
                       sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME)

    # save info to json file
    open(filename, 'w').write(dumps(data_manager_dict, sort_keys=True))


if __name__ == "__main__":
    main()

6:fa8c605bf385

#!/usr/bin/env python
# Dan Blankenberg
from __future__ import print_function

import json
import optparse
import os
import subprocess
import sys

DEFAULT_DATA_TABLE_NAME = "picard_indexes"


def get_id_name(params, dbkey, fasta_description=None):

    parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name')
    (options, args) = parser.parse_args()

    filename = args[0]

    with open(filename) as fh:
        params = json.load(fh)
    target_directory = params['output_data'][0]['extra_files_path']
    os.mkdir(target_directory)
    data_manager_dict = {}

    dbkey = options.fasta_dbkey

    # build the index
    build_picard_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id,
                       sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_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()