Mercurial > repos > iuc > data_manager_gemini_database_downloader
view 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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#!/usr/bin/env python import sys import os import json import shlex import datetime import subprocess def main(): today = datetime.date.today() gemini_root_dir = os.environ['GEMINI_ROOT_DIR'] params = json.loads( open( sys.argv[1] ).read() ) target_directory = params[ 'output_data' ][0]['extra_files_path'] os.mkdir( target_directory ) gemini_exec = os.path.join( gemini_root_dir, 'gemini', 'gemini', 'install-data.py' ) cmd = gemini_exec + " %s %s" % (' '.join( [params['param_dict']['gerp_bp'], params['param_dict']['cadd']] ), target_directory) #cmd = gemini_exec + " --help > %s/foo.txt" % target_directory ret = subprocess.check_call( cmd, shell=True ) data_manager_dict = { 'data_tables': {'gemini_databases': [ {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } ] } } #save info to json file with open( sys.argv[1], 'wb' ) as out: out.write( json.dumps( data_manager_dict ) ) if __name__ == "__main__": main()