Mercurial > repos > iuc > data_manager_snpsift_dbnsfp

comparison data_manager/data_manager_snpsift_dbnsfp.py @ 5:2cd22c2881e3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author iuc
date Tue, 30 Oct 2018 18:44:24 -0400
parents 5ebc15b0bf00
children 0a68ef0303c5
comparison
equal deleted inserted replaced
4:5ebc15b0bf00 5:2cd22c2881e3
41 41
42 data_table = 'snpsift_dbnsfps' 42 data_table = 'snpsift_dbnsfps'
43 softgenetics_url = 'ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/' 43 softgenetics_url = 'ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/'
44 dbNSFP_file_pat = '(dbNSFP(.*)_variant|dbscSNV(.*)).chr(.*)' 44 dbNSFP_file_pat = '(dbNSFP(.*)_variant|dbscSNV(.*)).chr(.*)'
45 tokenize = re.compile(r'(\d+)|(\D+)').findall 45 tokenize = re.compile(r'(\d+)|(\D+)').findall
46 dbNSFP_name_pat = 'dbNSFP(v|_light)?(\d*).*?' 46 dbNSFP_name_pat = r'dbNSFP(v|_light)?(\d*).*?'
47 47
48 48
49 def stop_err(msg): 49 def stop_err(msg):
50 sys.stderr.write(msg) 50 sys.stderr.write(msg)
51 sys.exit(1) 51 sys.exit(1)
52 52
53 53
54 def get_nsfp_genome_version(name): 54 def get_nsfp_genome_version(name):
55 genome_version = 'hg19' 55 genome_version = 'hg19'
56 dbNSFP_name_pat = '(dbscSNV|dbNSFP(v|_light)?)(\d*).*?' 56 dbNSFP_name_pat = r'(dbscSNV|dbNSFP(v|_light)?)(\d*).*?'
57 m = re.match(dbNSFP_name_pat, name) 57 m = re.match(dbNSFP_name_pat, name)
58 if m: 58 if m:
59 (base, mid, ver) = m.groups() 59 (base, mid, ver) = m.groups()
60 if base == 'dbscSNV': 60 if base == 'dbscSNV':
61 genome_version = 'hg19' 61 genome_version = 'hg19'
165 dbnsfp_tsv = None 165 dbnsfp_tsv = None
166 db_name = None 166 db_name = None
167 bzip_path = None 167 bzip_path = None
168 if options.softgenetics: 168 if options.softgenetics:
169 dbnsfp_url = softgenetics_url + options.softgenetics 169 dbnsfp_url = softgenetics_url + options.softgenetics
170 db_name = options.db_name if options.db_name else re.sub('\.zip$', '', options.softgenetics) 170 db_name = options.db_name if options.db_name else re.sub(r'\.zip$', '', options.softgenetics)
171 genome_version = get_nsfp_genome_version(options.softgenetics) 171 genome_version = get_nsfp_genome_version(options.softgenetics)
172 tsv = db_name + '.tsv' 172 tsv = db_name + '.tsv'
173 dbnsfp_tsv = download_dbnsfp_database(dbnsfp_url, tsv) 173 dbnsfp_tsv = download_dbnsfp_database(dbnsfp_url, tsv)
174 elif options.dbnsfp_tabular: 174 elif options.dbnsfp_tabular:
175 db_name = options.db_name 175 db_name = options.db_name