Mercurial > repos > iuc > data_manager_gemini_database_downloader
comparison data_manager/data_manager_gemini_download.py @ 0:fd9e9ac5ecb3 draft
Imported from capsule None
author | iuc |
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date | Mon, 25 Aug 2014 17:15:46 -0400 |
parents | |
children | 345412d58d75 |
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-1:000000000000 | 0:fd9e9ac5ecb3 |
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1 #!/usr/bin/env python | |
2 | |
3 import sys | |
4 import os | |
5 import json | |
6 import shlex | |
7 import datetime | |
8 import subprocess | |
9 | |
10 def main(): | |
11 | |
12 today = datetime.date.today() | |
13 gemini_root_dir = os.environ['GEMINI_ROOT_DIR'] | |
14 params = json.loads( open( sys.argv[1] ).read() ) | |
15 target_directory = params[ 'output_data' ][0]['extra_files_path'] | |
16 os.mkdir( target_directory ) | |
17 gemini_exec = os.path.join( gemini_root_dir, 'gemini', 'gemini', 'install-data.py' ) | |
18 cmd = gemini_exec + " %s %s" % (' '.join( [params['param_dict']['gerp_bp'], params['param_dict']['cadd']] ), target_directory) | |
19 #cmd = gemini_exec + " --help > %s/foo.txt" % target_directory | |
20 ret = subprocess.check_call( cmd, shell=True ) | |
21 data_manager_dict = { | |
22 'data_tables': | |
23 {'gemini_databases': [ | |
24 {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } | |
25 ] | |
26 } | |
27 } | |
28 | |
29 #save info to json file | |
30 with open( sys.argv[1], 'wb' ) as out: | |
31 out.write( json.dumps( data_manager_dict ) ) | |
32 | |
33 if __name__ == "__main__": | |
34 main() | |
35 |