comparison data_manager_monorail_index/data_manager/data_manager.py @ 3:1032e2599a5e draft

Uploaded

2:5615f4cee039

args = parser.parse_args()

def main(args):
    workdir = os.path.join(os.getcwd(), 'monorail_index')
    data_manager_entry = {}
    if args.name is None:
        args.name = args.url.split('/')[-1]
    data_manager_entry['value'] = args.name.lower()
    data_manager_entry['name'] = args.name
    data_manager_entry['path'] = args.output
    data_manager_json = dict(data_tables=dict(monorail_index=data_manager_entry))
    file(args.output, 'w').write(json.dumps(data_manager_json))

if __name__ == '__main__':
    main(args)

3:1032e2599a5e

args = parser.parse_args()

def main(args):
    workdir = os.path.join(os.getcwd(), 'monorail_index')
    data_manager_entry = {}
    ref = args.url.split('/')[-1]
    if args.name is None:
        args.name = ref
    data_manager_entry['value'] = args.name.lower()
    data_manager_entry['name'] = args.name
    jsonin = open(args.output).read()
    sys.stderr.write(jsonin)
    params = json.loads(jsonin)
    target_directory = params['output_data'][0]['extra_files_path']
    data_manager_entry['path'] = params['output_data'][0]['extra_files_path']
    data_manager_entry['exons_path'] = data_manager_entry['path'] + os.sep + ref + os.sep + 'gtf' + os.sep + 'exons.bed'
    data_manager_json = dict(data_tables=dict(monorail_index=data_manager_entry))
    file(args.output, 'w').write(json.dumps(data_manager_json))

if __name__ == '__main__':
    main(args)