0
|
1 #!/usr/bin/env python
|
|
2
|
|
3 import sys
|
|
4 import os
|
|
5 import re
|
|
6 import tempfile
|
|
7 import subprocess
|
|
8 import fileinput
|
|
9 import shutil
|
|
10 import optparse
|
|
11 import urllib2
|
|
12 from ftplib import FTP
|
|
13 import tarfile
|
|
14
|
|
15 from galaxy.util.json import from_json_string, to_json_string
|
|
16
|
|
17 def stop_err(msg):
|
|
18 sys.stderr.write(msg)
|
|
19 sys.exit(1)
|
|
20
|
|
21 """
|
|
22 # Download human database 'hg19'
|
|
23 java -jar snpEff.jar download -v hg19
|
|
24
|
|
25 <command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
|
|
26
|
|
27 snpEffectPredictor.bin
|
|
28 regulation_HeLa-S3.bin
|
|
29 regulation_pattern = 'regulation_(.+).bin'
|
|
30
|
|
31
|
|
32 """
|
|
33 def download_database(data_manager_dict, target_directory, jar_path,config,genome_version,organism):
|
|
34 ## get data_dir from config
|
|
35 ##---
|
|
36 ## Databases are stored here
|
|
37 ## E.g.: Information for 'hg19' is stored in data_dir/hg19/
|
|
38 ##
|
|
39 ## Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory
|
|
40 ##---
|
|
41 #data_dir = ~/snpEff/data/
|
|
42 data_dir = target_directory
|
|
43 (snpEff_dir,snpEff_jar) = os.path.split(jar_path)
|
|
44 args = [ 'java','-jar' ]
|
|
45 args.append( jar_path )
|
|
46 args.append( 'download' )
|
|
47 args.append( '-c' )
|
|
48 args.append( config )
|
|
49 args.append( '-dataDir' )
|
|
50 args.append( data_dir )
|
|
51 args.append( '-v' )
|
|
52 args.append( genome_version )
|
|
53 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir )
|
|
54 return_code = proc.wait()
|
|
55 if return_code:
|
|
56 sys.exit( return_code )
|
|
57 ## search data_dir/genome_version for files
|
|
58 regulation_pattern = 'regulation_(.+).bin'
|
|
59 # annotation files that are included in snpEff by a flag
|
|
60 annotations_dict = {'nextProt.bin' : '-nextprot','motif.bin': '-motif'}
|
|
61 genome_path = os.path.join(data_dir,genome_version)
|
|
62 if os.path.isdir(genome_path):
|
|
63 for root, dirs, files in os.walk(genome_path):
|
|
64 for fname in files:
|
|
65 if fname.startswith('snpEffectPredictor'):
|
|
66 # if snpEffectPredictor.bin download succeeded
|
|
67 name = genome_version + (' : ' + organism if organism else '')
|
|
68 data_table_entry = dict(value=genome_version, name=name, path=data_dir)
|
|
69 _add_data_table_entry( data_manager_dict, 'snpeff_genomedb', data_table_entry )
|
|
70 else:
|
|
71 m = re.match(regulation_pattern,fname)
|
|
72 if m:
|
|
73 name = m.groups()[0]
|
|
74 data_table_entry = dict(genome=genome_version,value=name, name=name)
|
|
75 _add_data_table_entry( data_manager_dict, 'snpeff_regulationdb', data_table_entry )
|
|
76 elif fname in annotations_dict:
|
|
77 value = annotations_dict[fname]
|
|
78 name = value.lstrip('-')
|
|
79 data_table_entry = dict(genome=genome_version,value=value, name=name)
|
|
80 _add_data_table_entry( data_manager_dict, 'snpeff_annotations', data_table_entry )
|
|
81 return data_manager_dict
|
|
82
|
|
83 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):
|
|
84 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
|
|
85 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
|
|
86 data_manager_dict['data_tables'][data_table].append( data_table_entry )
|
|
87 return data_manager_dict
|
|
88
|
|
89 def main():
|
|
90 #Parse Command Line
|
|
91 parser = optparse.OptionParser()
|
|
92 parser.add_option( '-j', '--jar_path', dest='jar_path', action='store', type="string", default=None, help='snpEff.jar path' )
|
|
93 parser.add_option( '-c', '--config', dest='config', action='store', type="string", default=None, help='snpEff.config path' )
|
|
94 parser.add_option( '-g', '--genome_version', dest='genome_version', action='store', type="string", default=None, help='genome_version' )
|
|
95 parser.add_option( '-o', '--organism', dest='organism', action='store', type="string", default=None, help='organism name' )
|
|
96 (options, args) = parser.parse_args()
|
|
97
|
|
98 filename = args[0]
|
|
99
|
|
100 params = from_json_string( open( filename ).read() )
|
|
101 target_directory = params[ 'output_data' ][0]['extra_files_path']
|
|
102 os.mkdir( target_directory )
|
|
103 data_manager_dict = {}
|
|
104
|
|
105
|
|
106 #Create SnpEff Reference Data
|
|
107 for genome_version, organism in zip(options.genome_version.split(','), options.organism.split(',')):
|
|
108 download_database( data_manager_dict, target_directory, options.jar_path, options.config, genome_version, organism )
|
|
109
|
|
110 #save info to json file
|
|
111 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
|
|
112
|
|
113 if __name__ == "__main__": main()
|
|
114
|