Mercurial > repos > iuc > data_manager_snpeff

comparison data_manager/data_manager_snpEff_databases.py @ 9:db4c810682ee draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
author iuc
date Tue, 24 Nov 2020 07:27:05 +0000
parents fbb459120c29
children
comparison
equal deleted inserted replaced
8:fbb459120c29 9:db4c810682ee
8 8
9 def fetch_databases(data_manager_dict, target_directory): 9 def fetch_databases(data_manager_dict, target_directory):
10 if not os.path.exists(target_directory): 10 if not os.path.exists(target_directory):
11 os.makedirs(target_directory) 11 os.makedirs(target_directory)
12 databases_path = os.path.join(target_directory, 'databases.out') 12 databases_path = os.path.join(target_directory, 'databases.out')
13 databases_output = open(databases_path, 'w')
14 args = ['snpEff', 'databases'] 13 args = ['snpEff', 'databases']
15 return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno()) 14 with open(databases_path, 'w') as databases_output:
15 return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno())
16 if return_code: 16 if return_code:
17 sys.exit(return_code) 17 sys.exit(return_code)
18 databases_output.close()
19 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {}) 18 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
20 data_manager_dict['data_tables']['snpeffv_databases'] = data_manager_dict['data_tables'].get('snpeffv_databases', []) 19 data_manager_dict['data_tables']['snpeffv_databases'] = data_manager_dict['data_tables'].get('snpeffv_databases', [])
21 data_table_entries = [] 20 data_table_entries = []
22 with open(databases_path, 'r') as fh: 21 with open(databases_path, 'r') as fh:
23 for i, line in enumerate(fh): 22 for line in fh:
24 fields = line.split('\t') 23 fields = line.split('\t')
25 if len(fields) >= 2: 24 if len(fields) >= 2:
26 genome_version = fields[0].strip() 25 genome_version = fields[0].strip()
27 if genome_version.startswith("Genome") or genome_version.startswith("-"): 26 if genome_version.startswith("Genome") or genome_version.startswith("-"):
28 continue 27 continue
39 parser = optparse.OptionParser() 38 parser = optparse.OptionParser()
40 (options, args) = parser.parse_args() 39 (options, args) = parser.parse_args()
41 40
42 filename = args[0] 41 filename = args[0]
43 42
44 params = json.loads(open(filename).read()) 43 with open(filename) as fh:
44 params = json.load(fh)
45 target_directory = params['output_data'][0]['extra_files_path'] 45 target_directory = params['output_data'][0]['extra_files_path']
46 os.mkdir(target_directory) 46 os.mkdir(target_directory)
47 data_manager_dict = {} 47 data_manager_dict = {}
48 48
49 # Create Defuse Reference Data 49 # Create Defuse Reference Data
50 data_manager_dict = fetch_databases(data_manager_dict, target_directory) 50 data_manager_dict = fetch_databases(data_manager_dict, target_directory)
51 51
52 # save info to json file 52 # save info to json file
53 open(filename, 'w').write(json.dumps(data_manager_dict, sort_keys=True)) 53 with open(filename, 'w') as fh:
54 json.dump(data_manager_dict, fh, sort_keys=True)
54 55
55 56
56 if __name__ == "__main__": 57 if __name__ == "__main__":
57 main() 58 main()