|
0
|
1 import json
|
|
|
2 import argparse
|
|
|
3 import os
|
|
|
4 import shutil
|
|
|
5
|
|
|
6
|
|
|
7
|
|
|
8 parser = argparse.ArgumentParser(description='Create data manager json.')
|
|
|
9 parser.add_argument('--dbkey', action='store')
|
|
|
10 parser.add_argument('--provider', action='store')
|
|
|
11 parser.add_argument('--ref', action='store')
|
|
|
12 parser.add_argument('--out', action='store')
|
|
|
13
|
|
|
14 args = parser.parse_args()
|
|
|
15
|
|
|
16 def main(args):
|
|
|
17 data_manager_entry = {}
|
|
|
18 data_manager_entry['value'] = args.dbkey.lower()
|
|
|
19 data_manager_entry['name'] = args.dbkey
|
|
|
20 data_manager_entry['path'] = '.'
|
|
|
21 data_manager_entry['ref'] = args.ref
|
|
|
22 data_manager_entry['provider'] = args.provider
|
|
|
23 data_manager_json = dict(data_tables=dict(gene_sets=data_manager_entry))
|
|
|
24 params = json.loads(open(args.out).read())
|
|
|
25 target_directory = params['output_data'][0]['extra_files_path']
|
|
|
26 os.mkdir(target_directory)
|
|
|
27 output_path = os.path.join(os.getcwd(), 'featurecount_gxf')
|
|
|
28 for filename in os.listdir(output_path):
|
|
|
29 shutil.move(os.path.join(output_path, filename), target_directory)
|
|
|
30 file(args.output, 'w').write(json.dumps(data_manager_json))
|
|
|
31
|
|
|
32 if __name__ == '__main__':
|
|
|
33 main(args)
|
