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