Mercurial > repos > iuc > data_manager_snpeff

comparison data_manager/data_manager_snpEff_databases.py @ 6:2107b4f40945 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit e32db0704e23d58358f749177988d2cb5f01c708
author iuc
date Tue, 18 Apr 2017 12:56:13 -0400
parents 3d9dd4b9fb09
children 08d7998c3afb
comparison
equal deleted inserted replaced
5:3d9dd4b9fb09 6:2107b4f40945
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']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_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:
29 # snpeff test genome 29 # snpeff test genome
30 if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'): 30 if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
31 continue 31 continue
32 description = fields[1].strip() + ' : ' + genome_version 32 description = fields[1].strip() + ' : ' + genome_version
33 data_table_entries.append(dict(value=genome_version, name=description)) 33 data_table_entries.append(dict(value=genome_version, name=description))
34 data_manager_dict['data_tables']['snpeff4_databases'] = data_table_entries 34 data_manager_dict['data_tables']['snpeffv_databases'] = data_table_entries
35 return data_manager_dict 35 return data_manager_dict
36 36
37 37
38 def main(): 38 def main():
39 parser = optparse.OptionParser() 39 parser = optparse.OptionParser()