annotate data_manager/data_manager_snpEff_databases.py @ 11:def511e8e005 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"

#!/usr/bin/env python
import json
import optparse
import os
import subprocess
import sys


def fetch_databases(data_manager_dict, target_directory):
    if not os.path.exists(target_directory):
        os.makedirs(target_directory)
    databases_path = os.path.join(target_directory, 'databases.out')
    args = ['snpEff', 'databases']
    with open(databases_path, 'w') as databases_output:
        return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno())
    if return_code:
        sys.exit(return_code)
    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
    data_manager_dict['data_tables']['snpeffv_databases'] = data_manager_dict['data_tables'].get('snpeffv_databases', [])
    data_table_entries = []
    with open(databases_path, 'r') as fh:
        for line in fh:
            fields = line.split('\t')
            if len(fields) >= 2:
                genome_version = fields[0].strip()
                if genome_version.startswith("Genome") or genome_version.startswith("-"):
                    continue
                # snpeff test genome
                if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
                    continue
                description = fields[1].strip() + ' : ' + genome_version
                data_table_entries.append(dict(value=genome_version, name=description))
    data_manager_dict['data_tables']['snpeffv_databases'] = data_table_entries
    return data_manager_dict


def main():
    parser = optparse.OptionParser()
    (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 = {}

    # Create Defuse Reference Data
    data_manager_dict = fetch_databases(data_manager_dict, target_directory)

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


if __name__ == "__main__":
    main()