Mercurial > repos > jjohnson > data_manager_snpeff

comparison data_manager/data_manager_snpEff_databases.py @ 6:a329eda0cdff draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jjohnson
date Wed, 09 Dec 2015 13:49:55 -0500
parents 78bcf4ac437c
children
comparison
equal deleted inserted replaced
5:78bcf4ac437c 6:a329eda0cdff
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
43 def fetch_databases(data_manager_dict, target_directory, jar_path): 21 def fetch_databases(data_manager_dict, target_directory, jar_path):
44 (snpEff_dir,snpEff_jar) = os.path.split(jar_path) 22 (snpEff_dir,snpEff_jar) = os.path.split(jar_path)
45 if not os.path.exists(target_directory): 23 if not os.path.exists(target_directory):
46 os.makedirs(target_directory) 24 os.makedirs(target_directory)
47 databases_path = os.path.join( target_directory, 'databases.out' ) 25 databases_path = os.path.join( target_directory, 'databases.out' )
55 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno() ) 33 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno() )
56 return_code = proc.wait() 34 return_code = proc.wait()
57 if return_code: 35 if return_code:
58 sys.exit( return_code ) 36 sys.exit( return_code )
59 databases_output.close() 37 databases_output.close()
60 snpeff_version = getSnpeffVersion(jar_path)
61 try: 38 try:
62 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) 39 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
63 data_manager_dict['data_tables']['snpeffv_databases'] = data_manager_dict['data_tables'].get( 'snpeffv_databases', [] ) 40 data_manager_dict['data_tables']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_databases', [] )
64 data_table_entries = [] 41 data_table_entries = []
65 fh = open(databases_path,'r') 42 fh = open(databases_path,'r')
66 for i,line in enumerate(fh): 43 for i,line in enumerate(fh):
67 fields = line.split('\t') 44 fields = line.split('\t')
68 if len(fields) >= 2: 45 if len(fields) >= 2:
71 continue 48 continue
72 #snpeff test genome 49 #snpeff test genome
73 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_'):
74 continue 51 continue
75 description = fields[1].strip() + ' : ' + genome_version 52 description = fields[1].strip() + ' : ' + genome_version
76 key = snpeff_version + '_' + genome_version 53 data_table_entries.append(dict(value=genome_version, name=description))
77 data_table_entries.append(dict(key=key, version=snpeff_version, value=genome_version, name=description)) 54 data_manager_dict['data_tables']['snpeff4_databases'] = data_table_entries
78 data_manager_dict['data_tables']['snpeffv_databases'] = data_table_entries
79 except Exception, e: 55 except Exception, e:
80 stop_err( 'Error parsing %s %s\n' % (config,str( e )) ) 56 stop_err( 'Error parsing %s %s\n' % (config,str( e )) )
81 else: 57 else:
82 fh.close() 58 fh.close()
83 return data_manager_dict 59 return data_manager_dict