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brentp / geneimpacts

prioritize effects of variant annotations from VEP, SnpEff, et al.
MIT License
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KeyError when using snpEff-annotated VCF with NextProt or Motif annotations #3

Closed bpow closed 8 years ago

bpow commented 8 years ago

The default annotations provided by snpEff include NextProt and Motif consequences. geneimpacts exits with a KeyError (in geneimpacts/effect.py line 557, for example: KeyError: 'NEXT_PROT[disulfide_bond]' when executing the line sevs = [IMPACT_SEVERITY[csq] for csq in self.consequences]) when these are present, since there is no entry in self.consequences for these effects.

brentp commented 8 years ago

Thanks for reporting and finding the cause. I'll update the gene impacts module can you send a vcf that recreates this problem?

bpow commented 8 years ago

Sure, here is a gist with a vcf file that demonstrates the error.

bpow commented 8 years ago

This may only be an issue when the snpEff '-classic' and '-formatEff' options are used, not with the newer ANN format.

brentp commented 8 years ago

this is fixed in c952623