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At first glance it's not clear why we want this method in addition to effects() that returns a VariantEffectCollection. Maybe consider getting rid of VariantEffectCollection, moving its methods into Variant, and having variant.effects() return the dict that is currently returned by transcript_effect_dict?
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VariantEffectCollection is gone on this branch, and all of its methods and properties (like this one) have migrated onto VariantCollection.
…initely not handling more than one amino acid of the new sequence
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This pull request started with just fixing the parsing logic in
maf.pyto deal with some of the edge cases of TCGA's various MAF files (spaces in values, non-standard capitalization of columns). In the process of adding unit tests I realized I wasn't handlingStopLossvariants at all incoding_effect.py, which may have been responsible for some errors I've seen while parsing larger germline VCF files.The branch eventually came to encompass a refactoring of
Variant, addition ofIntragenic&Intrageniceffects which don't require transcripts, and removal ofVariantEffectCollection(in favor of a simple list of variants and more effect-related helpers on theVariantitself).One of the MAF effect tests still doesn't work, but I guess there's a lot to start reviewing that probably won't be affected by remaining changes.