Mercurial > repos > sanbi-uwc > data_manager_shapeit_reference
diff data_manager/shapeit_ref.py @ 0:f86c65c60056 draft
planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
author | sanbi-uwc |
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date | Tue, 11 Sep 2018 10:39:38 -0400 |
parents | |
children | 52f0767fe68d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/shapeit_ref.py Tue Sep 11 10:39:38 2018 -0400 @@ -0,0 +1,47 @@ +#!/usr/bin/env python3 + +from __future__ import division, print_function +import argparse +import json +import os +import os.path + + +def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry): + data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {}) + data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, []) + data_manager_dict['data_tables'][data_table_name].append(data_table_entry) + return data_manager_dict + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='Generate a data manager output for SHAPEIT reference data') + parser.add_argument('key', help='Short key to identify this reference set (no spaces)') + parser.add_argument('description', help='Description of reference set') + parser.add_argument('path', help='Filesystem path to directory containing this reference set') + parser.add_argument('prefix', help='Filename prefix for files in this reference set') + parser.add_argument('output_file', type=argparse.FileType('w'), help='JSON file used to write data manager values to') + args = parser.parse_args() + + if not os.path.exists(args.path): + exit("Unable to find specified path {}".format(args.path)) + + prefix_exists = False + for filename in os.listdir(args.path): + if filename.startswith(args.prefix): + prefix_exists = True + break + else: + if not prefix_exists: + exit("Unable to find a file with prefix {} in {}".format(args.prefix, args.path)) + + for column in ('key', 'description', 'path', 'prefix'): + value = getattr(args, column) + if '\t' in value: + exit("TAB character found in {} argument".format(column)) + + data_manager_dict = {} + data_table_entry = dict(key=args.key, description=args.description, path=args.path, prefix=args.prefix) + _add_data_table_entry(data_manager_dict, 'shapeit_ref', data_table_entry) + + args.output_file.write(json.dumps(data_manager_dict) + '\n')