Mercurial > repos > jjohnson > ensembl_variant_report

comparison ensembl_variant_report.py @ 6:d9fad18ffdb1 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
author jjohnson
date Thu, 14 Jun 2018 17:50:33 -0400
parents 9e83cc05d384
children d5cb252c68da
comparison
equal deleted inserted replaced
5:9e83cc05d384 6:d9fad18ffdb1
111 if options.debug: print >> sys.stderr, "\n%s" % (fields) 111 if options.debug: print >> sys.stderr, "\n%s" % (fields)
112 (chrom, pos, id, ref, alts, qual, filter, info) = fields[0:8] 112 (chrom, pos, id, ref, alts, qual, filter, info) = fields[0:8]
113 alt_list = alts.split(',') 113 alt_list = alts.split(',')
114 pos = int(pos) 114 pos = int(pos)
115 qual = float(qual) 115 qual = float(qual)
116 dp = None
117 dpr = None
116 for info_item in info.split(';'): 118 for info_item in info.split(';'):
117 if info_item.find('=') < 0: continue 119 if info_item.find('=') < 0: continue
118 (key, val) = info_item.split('=', 1) 120 (key, val) = info_item.split('=', 1)
119 if key == 'DP': 121 if key == 'DP':
120 dp = int(val) 122 dp = int(val)
121 if key == 'DPR': 123 if key == 'DPR':
122 dpr = dpr = [int(x) for x in val.split(',')] 124 dpr = [int(x) for x in val.split(',')]
123 if key in ['EFF','ANN']: 125 if key in ['EFF','ANN']:
124 for effect in val.split(','): 126 for effect in val.split(','):
125 if options.debug: print >> sys.stderr, "\n%s" % (effect.split('|')) 127 if options.debug: print >> sys.stderr, "\n%s" % (effect.split('|'))
126 if key == 'ANN': 128 if key == 'ANN':
127 (alt,eff,impact,gene_name,gene_id,feature_type,transcript,biotype,exon,c_hgvs,p_hgvs,cdna,cds,aa,distance,info) = effect.split('|') 129 (alt,eff,impact,gene_name,gene_id,feature_type,transcript,biotype,exon,c_hgvs,p_hgvs,cdna,cds,aa,distance,info) = effect.split('|')