Handle `=` in synonymous variant names

griffithlab / civicpy

A python interface for the CIViC db application

MIT License

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Handle `=` in synonymous variant names #111

Closed susannasiebert closed 3 years ago

susannasiebert commented 3 years ago

CIViCpy check VCF fields for containing = and fails when such a variant is encountered because having a field value contain this character would break VCF specs since = has a special meaning for parsing. However, synonymous variants will legitimately contain this characters in their name (e.g. E55= (c.165G>A)). This PR implements a solution for this problem by replacing the = in the variant with the wildtype amino acid(s).

Closes #110.

susannasiebert commented 3 years ago

hgvs expressions are being encoded so they don't have this problem but we can switch to this implementation to make them look "nicer".

ahwagner commented 3 years ago

Okay. I'm fine with it either way–if you are happy with the current solution, I think it is good to merge!