Mercurial > repos > iuc > data_manager_snpeff

comparison data_manager/data_manager_snpEff_databases.py @ 9:08d7998c3afb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 036feef4f46b5aedabc5080c8fa4bc00d9c30d95"
author iuc
date Wed, 12 Feb 2020 18:33:53 -0500
parents 2107b4f40945
children c6fbc5421697
comparison
equal deleted inserted replaced
8:d107d20dc6bd 9:08d7998c3afb
7 7
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') 13 databases_output = open(databases_path, 'w')
14 args = ['snpEff', 'databases'] 14 args = ['snpEff', 'databases']
15 return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno()) 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() 18 databases_output.close()
19 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) 19 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', [] ) 20 data_manager_dict['data_tables']['snpeffv_databases'] = data_manager_dict['data_tables'].get('snpeffv_databases', [])
21 data_table_entries = [] 21 data_table_entries = []
22 with open(databases_path, 'r') as fh: 22 with open(databases_path, 'r') as fh:
23 for i, line in enumerate(fh): 23 for i, line in enumerate(fh):
24 fields = line.split('\t') 24 fields = line.split('\t')
25 if len(fields) >= 2: 25 if len(fields) >= 2:
39 parser = optparse.OptionParser() 39 parser = optparse.OptionParser()
40 (options, args) = parser.parse_args() 40 (options, args) = parser.parse_args()
41 41
42 filename = args[0] 42 filename = args[0]
43 43
44 params = json.loads( open( filename ).read() ) 44 params = json.loads(open(filename).read())
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, 'wb' ).write( json.dumps( data_manager_dict ) ) 53 open(filename, 'w').write(json.dumps(data_manager_dict, sort_keys=True))
54 54
55 55
56 if __name__ == "__main__": 56 if __name__ == "__main__":
57 main() 57 main()