Mercurial > repos > sanbi-uwc > data_manager_shapeit_reference
view 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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#!/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')