comparison data_manager/bowtie2_index_builder.py @ 10:e816eef8a48f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"

9:47432d88b0a0

#!/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_NAMES = ["bowtie2_indexes"]


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

    parser.add_option('-n', '--data_table_name', dest='data_table_name', action='append', 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_bowtie2_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES)

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


if __name__ == "__main__":
    main()

10:e816eef8a48f

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

import json
import optparse
import os
import subprocess
import sys

DEFAULT_DATA_TABLE_NAMES = ["bowtie2_indexes"]


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

    parser.add_option('-n', '--data_table_name', dest='data_table_name', action='append', 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_bowtie2_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES)

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


if __name__ == "__main__":
    main()