Mercurial > repos > iuc > data_manager_homer_preparse

comparison data_manager/homer_install_promoters.py @ 1:d9c177013aba draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
author iuc
date Thu, 06 Apr 2023 16:20:54 +0000
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0:e6a2110ac3b9 1:d9c177013aba
1 #!/usr/bin/env python
2
3 import json
4 import optparse
5 import shutil
6
7
8 def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
9 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
10 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
11 data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
12 return data_manager_dict
13
14
15 def main():
16 parser = optparse.OptionParser()
17 parser.add_option('-o', '--organism', dest='organism', action='store', type="string", default=None, help='organism')
18 parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name')
19 parser.add_option('-d', '--DB_path', dest='DB_path', action='store', type="string", default=None, help='DB_path')
20 parser.add_option('--organism_version', dest='organism_version', action='store', type="string", default=None, help='organism_version')
21 parser.add_option('--promoter_version', dest='promoter_version', action='store', type="string", default=None, help='promoter_version')
22 (options, args) = parser.parse_args()
23
24 # Get the target directory and move the data folder there
25 filename = args[0]
26 with open(filename) as fh:
27 params = json.load(fh)
28
29 target_directory = params['output_data'][0]['extra_files_path']
30 shutil.copytree(options.DB_path + '/data/accession', target_directory + '/accession')
31 shutil.copytree(options.DB_path + '/data/promoters', target_directory + '/promoters')
32 shutil.copyfile(options.DB_path + '/config.txt', target_directory + '/config.txt')
33
34 dbkey = str(options.organism) + '_o' + str(options.organism_version) + '_p' + str(options.promoter_version)
35 data_manager_dict = {}
36 data_table_entry = dict(value=dbkey, dbkey=dbkey, organism=options.organism, path=options.DB_path, organism_version=options.organism_version, promoter_version=options.promoter_version)
37 _add_data_table_entry(data_manager_dict, options.data_table_name, data_table_entry)
38
39 # Save info to json file
40 with open(filename, 'w') as fh:
41 json.dump(data_manager_dict, fh, sort_keys=True)
42
43
44 if __name__ == "__main__":
45 main()