Mercurial > repos > iuc > data_manager_snpeff
comparison data_manager/data_manager_snpEff_download.py @ 5:3d9dd4b9fb09 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
author | iuc |
---|---|
date | Tue, 18 Apr 2017 09:40:03 -0400 |
parents | 847b0f43c0e5 |
children | a6400027d849 |
comparison
equal
deleted
inserted
replaced
4:847b0f43c0e5 | 5:3d9dd4b9fb09 |
---|---|
1 #!/usr/bin/env python | 1 #!/usr/bin/env python |
2 import gzip | |
3 import json | 2 import json |
4 import optparse | 3 import optparse |
5 import os | 4 import os |
6 import re | 5 import re |
7 import subprocess | 6 import subprocess |
11 def stop_err(msg): | 10 def stop_err(msg): |
12 sys.stderr.write(msg) | 11 sys.stderr.write(msg) |
13 sys.exit(1) | 12 sys.exit(1) |
14 | 13 |
15 | 14 |
16 def fetch_databases(jar_path, genome_list=None): | 15 def fetch_databases(genome_list=None): |
17 snpDBs = dict() | 16 snpDBs = dict() |
18 (snpEff_dir, snpEff_jar) = os.path.split(jar_path) | |
19 databases_path = 'databases.out' | 17 databases_path = 'databases.out' |
20 databases_output = open(databases_path, 'w') | 18 databases_output = open(databases_path, 'w') |
21 args = [ 'java', '-jar' ] | 19 args = ['snpEff', 'databases'] |
22 args.append( snpEff_jar ) | 20 return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno()) |
23 args.append( 'databases' ) | |
24 # tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-snpEff-stderr" ) | |
25 # databases_output = open(databases_path) | |
26 # proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno(), stderr=tmp_stderr.fileno() ) | |
27 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno() ) | |
28 return_code = proc.wait() | |
29 if return_code: | 21 if return_code: |
30 sys.exit( return_code ) | 22 sys.exit( return_code ) |
31 databases_output.close() | 23 databases_output.close() |
32 try: | 24 try: |
33 fh = open(databases_path, 'r') | 25 fh = open(databases_path, 'r') |
46 else: | 38 else: |
47 fh.close() | 39 fh.close() |
48 return snpDBs | 40 return snpDBs |
49 | 41 |
50 | 42 |
51 def getOrganismNames(jar_path, genomes, organisms): | 43 def getOrganismNames(genomes, organisms): |
52 genome_list = genomes.split(',') | 44 genome_list = genomes.split(',') |
53 organism_list = organisms.split(',') if organisms else [] | 45 organism_list = organisms.split(',') if organisms else [] |
54 if len(genome_list) != len(organism_list): | 46 if len(genome_list) != len(organism_list): |
55 descriptions = [] | 47 descriptions = [] |
56 snpDBdict = fetch_databases(jar_path, genome_list=genome_list) | 48 snpDBdict = fetch_databases(genome_list=genome_list) |
57 for genome in snpDBdict: | 49 for genome in snpDBdict: |
58 descriptions.append(snpDBdict[genome] if genome in snpDBdict else genome) | 50 descriptions.append(snpDBdict[genome] if genome in snpDBdict else genome) |
59 return ','.join(descriptions) | 51 return ','.join(descriptions) |
60 return organisms | 52 return organisms |
61 | 53 |
62 | 54 |
63 def getSnpeffVersion(jar_path): | 55 def getSnpeffVersion(): |
64 snpeff_version = 'SnpEff ?.?' | 56 snpeff_version = 'SnpEff ?.?' |
65 (snpEff_dir, snpEff_jar) = os.path.split(jar_path) | |
66 stderr_path = 'snpeff.err' | 57 stderr_path = 'snpeff.err' |
67 stderr_fh = open(stderr_path, 'w') | 58 stderr_fh = open(stderr_path, 'w') |
68 args = [ 'java', '-jar' ] | 59 args = ['snpEff', '-h'] |
69 args.append( snpEff_jar ) | 60 return_code = subprocess.call(args=args, shell=False, stderr=stderr_fh.fileno()) |
70 args.append( '-h' ) | |
71 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stderr=stderr_fh.fileno() ) | |
72 return_code = proc.wait() | |
73 if return_code != 255: | 61 if return_code != 255: |
74 sys.exit( return_code ) | 62 sys.exit( return_code ) |
75 stderr_fh.close() | 63 stderr_fh.close() |
76 fh = open(stderr_path, 'r') | 64 fh = open(stderr_path, 'r') |
77 for line in fh: | 65 for line in fh: |
81 break | 69 break |
82 fh.close() | 70 fh.close() |
83 return snpeff_version | 71 return snpeff_version |
84 | 72 |
85 | 73 |
86 # Starting with SnpEff 4.1 the .bin files contain the SnpEff version: | |
87 # Example - the first 3 line of GRCh37.75/snpEffectPredictor.bin (uncompressed): | |
88 # | |
89 # SnpEff 4.1 | |
90 # CHROMOSOME 2 1 0 179197 GL000219.1 false | |
91 # CHROMOSOME 3 1 0 81347269 HSCHR17_1 false | |
92 def getSnpeffVersionFromFile(path): | |
93 snpeff_version = None | |
94 try: | |
95 fh = gzip.open(path, 'rb') | |
96 buf = fh.read(100) | |
97 lines = buf.splitlines() | |
98 m = re.match('^(SnpEff)\s+(\d+\.\d+).*$', lines[0].strip()) | |
99 if m: | |
100 snpeff_version = m.groups()[0] + m.groups()[1] | |
101 fh.close() | |
102 except Exception as e: | |
103 stop_err( 'Error parsing SnpEff version from: %s %s\n' % (path, str( e )) ) | |
104 return snpeff_version | |
105 | |
106 | |
107 # Download human database 'hg19' | 74 # Download human database 'hg19' |
108 # java -jar snpEff.jar download -v hg19 | 75 # java -jar snpEff.jar download -v hg19 |
109 # | 76 # |
110 # <command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> | 77 # <command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> |
111 # | 78 # |
112 # snpEffectPredictor.bin | 79 # snpEffectPredictor.bin |
113 # regulation_HeLa-S3.bin | 80 # regulation_HeLa-S3.bin |
114 # regulation_pattern = 'regulation_(.+).bin' | 81 # regulation_pattern = 'regulation_(.+).bin' |
115 def download_database(data_manager_dict, target_directory, jar_path, config, genome_version, organism): | 82 def download_database(data_manager_dict, target_directory, genome_version, organism): |
116 # get data_dir from config | 83 # get data_dir from config |
117 # --- | 84 # --- |
118 # Databases are stored here | 85 # Databases are stored here |
119 # E.g.: Information for 'hg19' is stored in data_dir/hg19/ | 86 # E.g.: Information for 'hg19' is stored in data_dir/hg19/ |
120 # | 87 # |
121 # Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory | 88 # Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory |
122 # --- | |
123 # data_dir = ~/snpEff/data/ | |
124 data_dir = target_directory | 89 data_dir = target_directory |
125 (snpEff_dir, snpEff_jar) = os.path.split(jar_path) | 90 args = ['snpEff', 'download', '-dataDir', data_dir, '-v', genome_version] |
126 args = [ 'java', '-jar' ] | 91 return_code = subprocess.call(args=args, shell=False) |
127 args.append( jar_path ) | |
128 args.append( 'download' ) | |
129 args.append( '-c' ) | |
130 args.append( config ) | |
131 args.append( '-dataDir' ) | |
132 args.append( data_dir ) | |
133 args.append( '-v' ) | |
134 args.append( genome_version ) | |
135 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir ) | |
136 return_code = proc.wait() | |
137 if return_code: | 92 if return_code: |
138 sys.exit( return_code ) | 93 sys.exit( return_code ) |
139 # search data_dir/genome_version for files | 94 # search data_dir/genome_version for files |
140 regulation_pattern = 'regulation_(.+).bin' | 95 regulation_pattern = 'regulation_(.+).bin' |
141 # annotation files that are included in snpEff by a flag | 96 # annotation files that are included in SnpEff by a flag |
142 annotations_dict = {'nextProt.bin': '-nextprot', 'motif.bin': '-motif'} | 97 annotations_dict = {'nextProt.bin': '-nextprot', 'motif.bin': '-motif', 'interactions.bin': '-interaction'} |
143 genome_path = os.path.join(data_dir, genome_version) | 98 genome_path = os.path.join(data_dir, genome_version) |
144 snpeff_version = getSnpeffVersion(jar_path) | 99 snpeff_version = getSnpeffVersion() |
145 key = snpeff_version + '_' + genome_version | 100 key = snpeff_version + '_' + genome_version |
146 if os.path.isdir(genome_path): | 101 if os.path.isdir(genome_path): |
147 for root, dirs, files in os.walk(genome_path): | 102 for root, dirs, files in os.walk(genome_path): |
148 for fname in files: | 103 for fname in files: |
149 if fname.startswith('snpEffectPredictor'): | 104 if fname.startswith('snpEffectPredictor'): |
150 # if snpEffectPredictor.bin download succeeded | 105 # if snpEffectPredictor.bin download succeeded |
151 name = genome_version + (' : ' + organism if organism else '') | 106 name = genome_version + (' : ' + organism if organism else '') |
152 # version = getSnpeffVersionFromFile(os.path.join(root,fname)) | |
153 data_table_entry = dict(key=key, version=snpeff_version, value=genome_version, name=name, path=data_dir) | 107 data_table_entry = dict(key=key, version=snpeff_version, value=genome_version, name=name, path=data_dir) |
154 _add_data_table_entry( data_manager_dict, 'snpeffv_genomedb', data_table_entry ) | 108 _add_data_table_entry( data_manager_dict, 'snpeffv_genomedb', data_table_entry ) |
155 else: | 109 else: |
156 m = re.match(regulation_pattern, fname) | 110 m = re.match(regulation_pattern, fname) |
157 if m: | 111 if m: |
172 data_manager_dict['data_tables'][data_table].append( data_table_entry ) | 126 data_manager_dict['data_tables'][data_table].append( data_table_entry ) |
173 return data_manager_dict | 127 return data_manager_dict |
174 | 128 |
175 | 129 |
176 def main(): | 130 def main(): |
177 # Parse Command Line | |
178 parser = optparse.OptionParser() | 131 parser = optparse.OptionParser() |
179 parser.add_option( '-j', '--jar_path', dest='jar_path', action='store', type="string", default=None, help='snpEff.jar path' ) | |
180 parser.add_option( '-c', '--config', dest='config', action='store', type="string", default=None, help='snpEff.config path' ) | |
181 parser.add_option( '-g', '--genome_version', dest='genome_version', action='store', type="string", default=None, help='genome_version' ) | 132 parser.add_option( '-g', '--genome_version', dest='genome_version', action='store', type="string", default=None, help='genome_version' ) |
182 parser.add_option( '-o', '--organism', dest='organism', action='store', type="string", default=None, help='organism name' ) | 133 parser.add_option( '-o', '--organism', dest='organism', action='store', type="string", default=None, help='organism name' ) |
183 (options, args) = parser.parse_args() | 134 (options, args) = parser.parse_args() |
184 | 135 |
185 filename = args[0] | 136 filename = args[0] |
188 target_directory = params[ 'output_data' ][0]['extra_files_path'] | 139 target_directory = params[ 'output_data' ][0]['extra_files_path'] |
189 os.mkdir( target_directory ) | 140 os.mkdir( target_directory ) |
190 data_manager_dict = {} | 141 data_manager_dict = {} |
191 | 142 |
192 # Create SnpEff Reference Data | 143 # Create SnpEff Reference Data |
193 for genome_version, organism in zip(options.genome_version.split(','), getOrganismNames(options.jar_path, options.genome_version, options.organism).split(',')): | 144 for genome_version, organism in zip(options.genome_version.split(','), getOrganismNames(options.genome_version, options.organism).split(',')): |
194 download_database( data_manager_dict, target_directory, options.jar_path, options.config, genome_version, organism ) | 145 download_database( data_manager_dict, target_directory, genome_version, organism ) |
195 | 146 |
196 # save info to json file | 147 # save info to json file |
197 open( filename, 'wb' ).write( json.dumps( data_manager_dict ) ) | 148 open( filename, 'wb' ).write( json.dumps( data_manager_dict ) ) |
198 | 149 |
199 | 150 |