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comparison data_manager/data_manager_snpEff_databases.py @ 6:eb394dd65c98

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Add mutli-select to data managers from Bjoern, filter unique database options in snpEff_download.xml snpEff.xml
author Jim Johnson <jj@umn.edu>
date Thu, 28 Nov 2013 08:16:11 -0600
parents 6ad9205c1307
children
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5:8952990fcab9 6:eb394dd65c98
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:
46 genome_version = fields[0].strip() 46 genome_version = fields[0].strip()
47 if genome_version.startswith("Genome") or genome_version.startswith("-"): 47 if genome_version.startswith("Genome") or genome_version.startswith("-"):
48 continue
49 #snpeff test genome
50 if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
48 continue 51 continue
49 description = fields[1].strip() + ' : ' + genome_version 52 description = fields[1].strip() + ' : ' + genome_version
50 data_table_entries.append(dict(value=genome_version, name=description)) 53 data_table_entries.append(dict(value=genome_version, name=description))
51 data_manager_dict['data_tables']['snpeff_databases'] = data_table_entries 54 data_manager_dict['data_tables']['snpeff_databases'] = data_table_entries
52 except Exception, e: 55 except Exception, e:
53 stop_err( 'Error parsing %s %s\n' % (config,str( e )) ) 56 stop_err( 'Error parsing %s %s\n' % (config,str( e )) )
54 else: 57 else:
55 fh.close() 58 fh.close()
56 return data_manager_dict 59 return data_manager_dict