Mercurial > repos > iuc > snpeff
comparison data_manager/data_manager_snpEff_download.py @ 0:e8adfc4c0a6b draft
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author | iuc |
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date | Wed, 11 Dec 2013 08:53:32 -0500 |
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-1:000000000000 | 0:e8adfc4c0a6b |
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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 |