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comparison data_manager/data_manager_snpEff_databases.py @ 3:c6769a700e55

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Update loc data to separate version 4 databases
author Jim Johnson <jj@umn.edu>
date Tue, 21 Oct 2014 14:04:33 -0500
parents bc50aa3b328a
children 78bcf4ac437c
comparison
equal deleted inserted replaced
2:5a01e5cfa6bc 3:c6769a700e55
35 if return_code: 35 if return_code:
36 sys.exit( return_code ) 36 sys.exit( return_code )
37 databases_output.close() 37 databases_output.close()
38 try: 38 try:
39 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) 39 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
40 data_manager_dict['data_tables']['snpeff_databases'] = data_manager_dict['data_tables'].get( 'snpeff_databases', [] ) 40 data_manager_dict['data_tables']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_databases', [] )
41 data_table_entries = [] 41 data_table_entries = []
42 fh = open(databases_path,'r') 42 fh = open(databases_path,'r')
43 for i,line in enumerate(fh): 43 for i,line in enumerate(fh):
44 fields = line.split('\t') 44 fields = line.split('\t')
45 if len(fields) >= 2: 45 if len(fields) >= 2:
49 #snpeff test genome 49 #snpeff test genome
50 if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'): 50 if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
51 continue 51 continue
52 description = fields[1].strip() + ' : ' + genome_version 52 description = fields[1].strip() + ' : ' + genome_version
53 data_table_entries.append(dict(value=genome_version, name=description)) 53 data_table_entries.append(dict(value=genome_version, name=description))
54 data_manager_dict['data_tables']['snpeff_databases'] = data_table_entries 54 data_manager_dict['data_tables']['snpeff4_databases'] = data_table_entries
55 except Exception, e: 55 except Exception, e:
56 stop_err( 'Error parsing %s %s\n' % (config,str( e )) ) 56 stop_err( 'Error parsing %s %s\n' % (config,str( e )) )
57 else: 57 else:
58 fh.close() 58 fh.close()
59 return data_manager_dict 59 return data_manager_dict