Mercurial > repos > sanbi-uwc > data_manager_shapeit_reference
comparison 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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-1:000000000000 | 0:f86c65c60056 |
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1 #!/usr/bin/env python3 | |
2 | |
3 from __future__ import division, print_function | |
4 import argparse | |
5 import json | |
6 import os | |
7 import os.path | |
8 | |
9 | |
10 def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry): | |
11 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {}) | |
12 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, []) | |
13 data_manager_dict['data_tables'][data_table_name].append(data_table_entry) | |
14 return data_manager_dict | |
15 | |
16 | |
17 if __name__ == '__main__': | |
18 parser = argparse.ArgumentParser(description='Generate a data manager output for SHAPEIT reference data') | |
19 parser.add_argument('key', help='Short key to identify this reference set (no spaces)') | |
20 parser.add_argument('description', help='Description of reference set') | |
21 parser.add_argument('path', help='Filesystem path to directory containing this reference set') | |
22 parser.add_argument('prefix', help='Filename prefix for files in this reference set') | |
23 parser.add_argument('output_file', type=argparse.FileType('w'), help='JSON file used to write data manager values to') | |
24 args = parser.parse_args() | |
25 | |
26 if not os.path.exists(args.path): | |
27 exit("Unable to find specified path {}".format(args.path)) | |
28 | |
29 prefix_exists = False | |
30 for filename in os.listdir(args.path): | |
31 if filename.startswith(args.prefix): | |
32 prefix_exists = True | |
33 break | |
34 else: | |
35 if not prefix_exists: | |
36 exit("Unable to find a file with prefix {} in {}".format(args.prefix, args.path)) | |
37 | |
38 for column in ('key', 'description', 'path', 'prefix'): | |
39 value = getattr(args, column) | |
40 if '\t' in value: | |
41 exit("TAB character found in {} argument".format(column)) | |
42 | |
43 data_manager_dict = {} | |
44 data_table_entry = dict(key=args.key, description=args.description, path=args.path, prefix=args.prefix) | |
45 _add_data_table_entry(data_manager_dict, 'shapeit_ref', data_table_entry) | |
46 | |
47 args.output_file.write(json.dumps(data_manager_dict) + '\n') |