view data_manager/rna_star_index_builder.py @ 0:e23440b3332a draft

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#!/usr/bin/env python

import argparse
import json


def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('--config-file')
    parser.add_argument('--value')
    parser.add_argument('--dbkey')
    parser.add_argument('--name')
    parser.add_argument('--subdir')
    parser.add_argument('--data-table')
    parser.add_argument('--with-gene-model', action='store_true')
    parser.add_argument('--index-version')

    args = parser.parse_args()

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

    with_gene_model = "0"
    if args.with_gene_model:
        with_gene_model = "1"

    data_manager_dict = {
        'data_tables': {
            args.data_table: [
                {
                    "value": args.value,
                    "dbkey": args.dbkey,
                    "name": args.name,
                    "path": args.subdir,
                    "with_gene_model": with_gene_model,
                    "version": args.index_version
                }
            ]
        }
    }
    with open(args.config_file, 'w') as fh:
        json.dump(data_manager_dict, fh, sort_keys=True)


if __name__ == "__main__":
    main()