Mercurial > repos > iuc > data_manager_snpsift_dbnsfp
comparison data_manager/data_manager_snpsift_dbnsfp.py @ 0:0e9e3bb5776a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
author | iuc |
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date | Tue, 07 Jun 2016 10:23:16 -0400 |
parents | |
children | 3d4cd0e3891f |
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-1:000000000000 | 0:0e9e3bb5776a |
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1 #!/usr/bin/env python | |
2 | |
3 import gzip | |
4 import json | |
5 import optparse | |
6 import os | |
7 import os.path | |
8 import re | |
9 import shutil | |
10 import sys | |
11 import urllib | |
12 import zipfile | |
13 | |
14 from pysam import ctabix | |
15 | |
16 """ | |
17 # Install dbNSFP databases | |
18 # from DbNsfp site | |
19 # Download dbNSFP database | |
20 $ wget ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/dbNSFPv2.4.zip | |
21 # Uncompress | |
22 $ unzip dbNSFP2.4.zip | |
23 # Create a single file version | |
24 $ (head -n 1 dbNSFP2.4_variant.chr1 ; cat dbNSFP2.4_variant.chr* | grep -v "^#") > dbNSFP2.4.txt | |
25 # Compress using block-gzip algorithm | |
26 bgzip dbNSFP2.4.txt | |
27 # Create tabix index | |
28 tabix -s 1 -b 2 -e 2 dbNSFP2.4.txt.gz | |
29 | |
30 data_table: | |
31 | |
32 <table name="snpsift_dbnsfps" comment_char="#"> | |
33 <columns>key, build, name, value, annotations</columns> | |
34 <file path="tool-data/snpsift_dbnsfps.loc" /> | |
35 </table> | |
36 | |
37 #id build description path annotations | |
38 #GRCh37_dbNSFP2.4 GRCh37 GRCh37 dbNSFP2.4 /depot/snpeff/dbNSFP2.4.gz SIFT_pred,Uniprot_acc | |
39 #GRCh38_dbNSFP2.7 GRCh38 GRCh38 dbNSFP2.7 /depot/snpeff/dbNSFP2.7.gz SIFT_pred,Uniprot_acc | |
40 """ | |
41 | |
42 data_table = 'snpsift_dbnsfps' | |
43 softgenetics_url = 'ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/' | |
44 dbNSFP_file_pat = '(dbNSFP(.*)_variant|dbscSNV(.*)).chr(.*)' | |
45 tokenize = re.compile(r'(\d+)|(\D+)').findall | |
46 dbNSFP_name_pat = 'dbNSFP(v|_light)?(\d*).*?' | |
47 | |
48 | |
49 def stop_err(msg): | |
50 sys.stderr.write(msg) | |
51 sys.exit(1) | |
52 | |
53 | |
54 def get_nsfp_genome_version(name): | |
55 genome_version = 'hg19' | |
56 dbNSFP_name_pat = '(dbscSNV|dbNSFP(v|_light)?)(\d*).*?' | |
57 m = re.match(dbNSFP_name_pat, name) | |
58 if m: | |
59 (base, mid, ver) = m.groups() | |
60 if base == 'dbscSNV': | |
61 genome_version = 'hg19' | |
62 else: | |
63 genome_version = 'hg38' if ver == '3' else 'hg19' if ver == '2' else 'hg18' | |
64 return genome_version | |
65 | |
66 | |
67 def get_annotations(gzip_path): | |
68 annotations = None | |
69 fh = None | |
70 try: | |
71 fh = gzip.open(gzip_path, 'r') | |
72 buf = fh.read(10000) | |
73 lines = buf.splitlines() | |
74 headers = lines[0].split('\t') | |
75 annotations = ','.join([x.strip() for x in headers[4:]]) | |
76 except Exception as e: | |
77 stop_err('Error Reading annotations %s : %s' % (gzip_path, e)) | |
78 finally: | |
79 if fh: | |
80 fh.close() | |
81 return annotations | |
82 | |
83 | |
84 def tabix_file(input_fname, output_fname): | |
85 print >> sys.stdout, "tabix_file: %s -> %s" % (input_fname, output_fname) | |
86 ctabix.tabix_compress(input_fname, output_fname, force=True) | |
87 # Column indices are 0-based. | |
88 ctabix.tabix_index(output_fname, seq_col=0, start_col=1, end_col=1) | |
89 | |
90 | |
91 def natural_sortkey(string): | |
92 return tuple(int(num) if num else alpha for num, alpha in tokenize(string)) | |
93 | |
94 | |
95 def download_dbnsfp_database(url, output_file): | |
96 dbnsfp_tsv = None | |
97 file_path = 'downloaded_file' | |
98 urllib.urlretrieve(url, file_path) | |
99 with zipfile.ZipFile(file_path, 'r') as my_zip: | |
100 dbnsfp_tsv = output_file if output_file else 'dbnsfp_tsv' | |
101 wtr = open(dbnsfp_tsv, 'w') | |
102 allfiles = [info.filename for info in my_zip.infolist()] | |
103 files = [f for f in allfiles if re.match(dbNSFP_file_pat, f)] | |
104 files = sorted(files, key=natural_sortkey) | |
105 for j, file in enumerate(files): | |
106 fh = my_zip.open(file, 'rU') | |
107 for i, line in enumerate(fh): | |
108 if j > 0 and i == 0: | |
109 continue | |
110 wtr.write(line) | |
111 return dbnsfp_tsv | |
112 | |
113 | |
114 def main(): | |
115 # Parse Command Line | |
116 parser = optparse.OptionParser() | |
117 parser.add_option('-g', '--dbkey', dest='dbkey', action='store', type="string", default=None, help='dbkey genome version') | |
118 parser.add_option('-n', '--db_name', dest='db_name', action='store', type="string", default=None, help='A name for a history snpsiftdbnsfp dataset') | |
119 parser.add_option('-s', '--softgenetics', dest='softgenetics', action='store', type="string", default=None, help='A name for softgenetics dbNSFP file') | |
120 parser.add_option('-H', '--snpsiftdbnsfp', dest='snpsiftdbnsfp', action='store', type="string", default=None, help='A history snpsiftdbnsfp dataset') | |
121 parser.add_option('-T', '--dbnsfp_tabular', dest='dbnsfp_tabular', action='store', type="string", default=None, help='A history dbnsfp_tabular dataset') | |
122 (options, args) = parser.parse_args() | |
123 | |
124 filename = args[0] | |
125 params = json.loads(open(filename).read()) | |
126 target_directory = params['output_data'][0]['extra_files_path'] | |
127 if not os.path.exists(target_directory): | |
128 os.mkdir(target_directory) | |
129 data_manager_dict = {} | |
130 genome_version = options.dbkey if options.dbkey else 'unknown' | |
131 dbnsfp_tsv = None | |
132 db_name = None | |
133 bzip_path = None | |
134 if options.softgenetics: | |
135 dbnsfp_url = softgenetics_url + options.softgenetics | |
136 db_name = options.db_name if options.db_name else re.sub('\.zip$', '', options.softgenetics) | |
137 genome_version = get_nsfp_genome_version(options.softgenetics) | |
138 tsv = db_name + '.tsv' | |
139 dbnsfp_tsv = download_dbnsfp_database(dbnsfp_url, tsv) | |
140 elif options.dbnsfp_tabular: | |
141 db_name = options.db_name | |
142 dbnsfp_tsv = options.dbnsfp_tabular | |
143 elif options.snpsiftdbnsfp: | |
144 (dirpath, bgzip_name) = os.path.split(options.snpsiftdbnsfp) | |
145 idxpath = options.snpsiftdbnsfp + '.tbi' | |
146 shutil.copy(options.snpsiftdbnsfp, target_directory) | |
147 shutil.copy(idxpath, target_directory) | |
148 bzip_path = os.path.join(target_directory, bgzip_name) | |
149 db_name = re.sub('(.txt)?.gz$', '', bgzip_name) | |
150 else: | |
151 stop_err('Either --softgenetics or --dbnsfp_tabular required') | |
152 if dbnsfp_tsv: | |
153 bgzip_name = '%s.txt.gz' % db_name | |
154 bzip_path = os.path.join(target_directory, bgzip_name) | |
155 tabix_file(dbnsfp_tsv, bzip_path) | |
156 annotations = get_annotations(bzip_path) | |
157 # Create the SnpSift dbNSFP Reference Data | |
158 data_table_entry = dict(key='%s_%s' % (genome_version, db_name), build=genome_version, name='%s %s' % (genome_version, db_name), value=bgzip_name, annotations=annotations) | |
159 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {}) | |
160 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get(data_table, []) | |
161 data_manager_dict['data_tables'][data_table].append(data_table_entry) | |
162 | |
163 # save info to json file | |
164 open(filename, 'wb').write(json.dumps(data_manager_dict)) | |
165 | |
166 if __name__ == "__main__": | |
167 main() |