| Previous changeset 0:fcb7188fa0d2 (2014-02-07) |
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Commit message:
Check for both classic and sequence_ontology name for EFF: "NON_SYNONYMOUS_CODING" or "missense_variant" |
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modified:
snpeff_to_peptides.py |
| b |
| diff -r fcb7188fa0d2 -r 80eff5812b2a snpeff_to_peptides.py --- a/snpeff_to_peptides.py Fri Feb 07 15:05:20 2014 -0500 +++ b/snpeff_to_peptides.py Thu Nov 06 13:57:31 2014 -0600 |
| [ |
| @@ -187,7 +187,7 @@ effects = val.split(',') for effect in effects: (eff,effs) = effect.rstrip(')').split('(') - if not eff == 'NON_SYNONYMOUS_CODING': + if not (eff == 'NON_SYNONYMOUS_CODING' or eff == 'missense_variant'): continue eff_fields = effs.split('|') (impact,functional_class,codon_change,aa_change,aa_len,gene_name,biotype,coding,transcript,exon) = eff_fields[0:10] |