Mercurial > repos > jjohnson > snpeff

comparison data_manager/data_manager_snpEff_download.py @ 5:8952990fcab9

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
author Jim Johnson <jj@umn.edu>
date Wed, 27 Nov 2013 09:11:32 -0600
parents 6ad9205c1307
children eb394dd65c98
comparison
equal deleted inserted replaced
4:47ddc9f4d0b6 5:8952990fcab9
37 ## E.g.: Information for 'hg19' is stored in data_dir/hg19/ 37 ## E.g.: Information for 'hg19' is stored in data_dir/hg19/
38 ## 38 ##
39 ## Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory 39 ## Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory
40 ##--- 40 ##---
41 #data_dir = ~/snpEff/data/ 41 #data_dir = ~/snpEff/data/
42 data_dir = None 42 data_dir = target_directory
43 try:
44 fh = open(config)
45 for i,line in enumerate(fh):
46 if line.strip().startswith('data_dir'):
47 (k,v) = line.split('=')
48 data_dir = os.path.expanduser(v.strip())
49 break
50 except Exception, e:
51 stop_err( 'Error parsing %s %s\n' % (config,str( e )) )
52 else:
53 fh.close()
54 (snpEff_dir,snpEff_jar) = os.path.split(jar_path) 43 (snpEff_dir,snpEff_jar) = os.path.split(jar_path)
55 args = [ 'java','-jar' ] 44 args = [ 'java','-jar' ]
56 args.append( jar_path ) 45 args.append( jar_path )
57 args.append( 'download' ) 46 args.append( 'download' )
58 # args.append( '-c' ) 47 args.append( '-c' )
59 # args.append( 'config' ) 48 args.append( config )
49 args.append( '-dataDir' )
50 args.append( data_dir )
60 args.append( '-v' ) 51 args.append( '-v' )
61 args.append( genome_version ) 52 args.append( genome_version )
62 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir ) 53 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir )
63 return_code = proc.wait() 54 return_code = proc.wait()
64 if return_code: 55 if return_code:
72 for root, dirs, files in os.walk(genome_path): 63 for root, dirs, files in os.walk(genome_path):
73 for fname in files: 64 for fname in files:
74 if fname.startswith('snpEffectPredictor'): 65 if fname.startswith('snpEffectPredictor'):
75 # if snpEffectPredictor.bin download succeeded 66 # if snpEffectPredictor.bin download succeeded
76 name = genome_version + (' : ' + organism if organism else '') 67 name = genome_version + (' : ' + organism if organism else '')
77 data_table_entry = dict(value=genome_version, name=name) 68 data_table_entry = dict(value=genome_version, name=name, path=data_dir)
78 _add_data_table_entry( data_manager_dict, 'snpeff_genomedb', data_table_entry ) 69 _add_data_table_entry( data_manager_dict, 'snpeff_genomedb', data_table_entry )
79 else: 70 else:
80 m = re.match(regulation_pattern,fname) 71 m = re.match(regulation_pattern,fname)
81 if m: 72 if m:
82 name = m.groups()[0] 73 name = m.groups()[0]