Mercurial > repos > jjohnson > data_manager_snpeff

comparison data_manager/data_manager_snpEff_databases.py @ 5:78bcf4ac437c

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Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file
author Jim Johnson <jj@umn.edu>
date Tue, 13 Jan 2015 12:54:20 -0600
parents c6769a700e55
children a329eda0cdff
comparison
equal deleted inserted replaced
4:6a378d0f4856 5:78bcf4ac437c
16 16
17 def stop_err(msg): 17 def stop_err(msg):
18 sys.stderr.write(msg) 18 sys.stderr.write(msg)
19 sys.exit(1) 19 sys.exit(1)
20 20
21 def getSnpeffVersion(jar_path):
22 snpeff_version = 'SnpEff ?.?'
23 (snpEff_dir,snpEff_jar) = os.path.split(jar_path)
24 stderr_path = 'snpeff.err'
25 stderr_fh = open(stderr_path,'w')
26 args = [ 'java','-jar', ]
27 args.append( snpEff_jar )
28 args.append( '-h' )
29 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stderr=stderr_fh.fileno() )
30 return_code = proc.wait()
31 if return_code != 255:
32 sys.exit( return_code )
33 stderr_fh.close()
34 fh = open(stderr_path,'r')
35 for line in fh:
36 m = re.match('^[Ss]npEff version (SnpEff)\s*(\d+\.\d+).*$',line)
37 if m:
38 snpeff_version = m.groups()[0] + m.groups()[1]
39 break
40 fh.close()
41 return snpeff_version
42
21 def fetch_databases(data_manager_dict, target_directory, jar_path): 43 def fetch_databases(data_manager_dict, target_directory, jar_path):
22 (snpEff_dir,snpEff_jar) = os.path.split(jar_path) 44 (snpEff_dir,snpEff_jar) = os.path.split(jar_path)
23 if not os.path.exists(target_directory): 45 if not os.path.exists(target_directory):
24 os.makedirs(target_directory) 46 os.makedirs(target_directory)
25 databases_path = os.path.join( target_directory, 'databases.out' ) 47 databases_path = os.path.join( target_directory, 'databases.out' )
33 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno() ) 55 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno() )
34 return_code = proc.wait() 56 return_code = proc.wait()
35 if return_code: 57 if return_code:
36 sys.exit( return_code ) 58 sys.exit( return_code )
37 databases_output.close() 59 databases_output.close()
60 snpeff_version = getSnpeffVersion(jar_path)
38 try: 61 try:
39 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) 62 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
40 data_manager_dict['data_tables']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_databases', [] ) 63 data_manager_dict['data_tables']['snpeffv_databases'] = data_manager_dict['data_tables'].get( 'snpeffv_databases', [] )
41 data_table_entries = [] 64 data_table_entries = []
42 fh = open(databases_path,'r') 65 fh = open(databases_path,'r')
43 for i,line in enumerate(fh): 66 for i,line in enumerate(fh):
44 fields = line.split('\t') 67 fields = line.split('\t')
45 if len(fields) >= 2: 68 if len(fields) >= 2:
48 continue 71 continue
49 #snpeff test genome 72 #snpeff test genome
50 if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'): 73 if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
51 continue 74 continue
52 description = fields[1].strip() + ' : ' + genome_version 75 description = fields[1].strip() + ' : ' + genome_version
53 data_table_entries.append(dict(value=genome_version, name=description)) 76 key = snpeff_version + '_' + genome_version
54 data_manager_dict['data_tables']['snpeff4_databases'] = data_table_entries 77 data_table_entries.append(dict(key=key, version=snpeff_version, value=genome_version, name=description))
78 data_manager_dict['data_tables']['snpeffv_databases'] = data_table_entries
55 except Exception, e: 79 except Exception, e:
56 stop_err( 'Error parsing %s %s\n' % (config,str( e )) ) 80 stop_err( 'Error parsing %s %s\n' % (config,str( e )) )
57 else: 81 else:
58 fh.close() 82 fh.close()
59 return data_manager_dict 83 return data_manager_dict