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comparison snpeff_to_peptides.py @ 1:80eff5812b2a default tip

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Check for both classic and sequence_ontology name for EFF: "NON_SYNONYMOUS_CODING" or "missense_variant"
author Jim Johnson <jj@umn.edu>
date Thu, 06 Nov 2014 13:57:31 -0600
parents fcb7188fa0d2
children
comparison
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0:fcb7188fa0d2 1:80eff5812b2a
185 (key,val) = info_item.split('=',1) 185 (key,val) = info_item.split('=',1)
186 if key == 'EFF': 186 if key == 'EFF':
187 effects = val.split(',') 187 effects = val.split(',')
188 for effect in effects: 188 for effect in effects:
189 (eff,effs) = effect.rstrip(')').split('(') 189 (eff,effs) = effect.rstrip(')').split('(')
190 if not eff == 'NON_SYNONYMOUS_CODING': 190 if not (eff == 'NON_SYNONYMOUS_CODING' or eff == 'missense_variant'):
191 continue 191 continue
192 eff_fields = effs.split('|') 192 eff_fields = effs.split('|')
193 (impact,functional_class,codon_change,aa_change,aa_len,gene_name,biotype,coding,transcript,exon) = eff_fields[0:10] 193 (impact,functional_class,codon_change,aa_change,aa_len,gene_name,biotype,coding,transcript,exon) = eff_fields[0:10]
194 if transcript: 194 if transcript:
195 aa_pos = None # 1-based position 195 aa_pos = None # 1-based position