Mercurial > repos > cschu > featurecounts_data_manager
diff gffdm/data_manager/make_json.py @ 2:b3cd759a0064 draft default tip
Uploaded
author | cschu |
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date | Sun, 26 Jun 2016 17:04:24 -0400 |
parents | a297bbcd1c01 |
children |
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--- a/gffdm/data_manager/make_json.py Sun Jun 26 16:58:34 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ -import json -import argparse -import os -import shutil - - - -parser = argparse.ArgumentParser(description='Create data manager json.') -parser.add_argument('--dbkey', action='store') -parser.add_argument('--provider', action='store') -parser.add_argument('--ref', action='store') -parser.add_argument('--out', action='store') - -args = parser.parse_args() - -def main(args): - data_manager_entry = {} - data_manager_entry['value'] = args.dbkey.lower() - data_manager_entry['name'] = args.dbkey - data_manager_entry['path'] = '.' - data_manager_entry['ref'] = args.ref - data_manager_entry['provider'] = args.provider - data_manager_json = dict(data_tables=dict(gene_sets=data_manager_entry)) - params = json.loads(open(args.out).read()) - target_directory = params['output_data'][0]['extra_files_path'] - os.mkdir(target_directory) - output_path = os.path.join(os.getcwd(), 'featurecount_gxf') - for filename in os.listdir(output_path): - shutil.move(os.path.join(output_path, filename), target_directory) - file(args.output, 'w').write(json.dumps(data_manager_json)) - -if __name__ == '__main__': - main(args)