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1 #!/usr/bin/env python
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2
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3 import sys
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4 import os
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5 import json
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6 import shlex
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7 import datetime
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8 import subprocess
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9
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10 def main():
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11
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12 today = datetime.date.today()
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13 gemini_root_dir = os.environ['GEMINI_ROOT_DIR']
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14 params = json.loads( open( sys.argv[1] ).read() )
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15 target_directory = params[ 'output_data' ][0]['extra_files_path']
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16 os.mkdir( target_directory )
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17 gemini_exec = os.path.join( gemini_root_dir, 'gemini', 'gemini', 'install-data.py' )
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18 cmd = gemini_exec + " %s %s" % (' '.join( [params['param_dict']['gerp_bp'], params['param_dict']['cadd']] ), target_directory)
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19 #cmd = gemini_exec + " --help > %s/foo.txt" % target_directory
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20 ret = subprocess.check_call( cmd, shell=True )
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21 data_manager_dict = {
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22 'data_tables':
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23 {'gemini_databases': [
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24 {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() }
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25 ]
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26 }
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27 }
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28
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29 #save info to json file
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30 with open( sys.argv[1], 'wb' ) as out:
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31 out.write( json.dumps( data_manager_dict ) )
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32
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33 if __name__ == "__main__":
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34 main()
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35
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