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
date Tue, 11 Sep 2018 10:39:38 -0400
parents
children 52f0767fe68d
comparison
equal deleted inserted replaced
-1:000000000000 0:f86c65c60056
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')