biocommons/hgvs

Support transcript identifiers (in parentheses) in variants

marius-mather opened this issue · 1 comments

The HGVS nomenclature now recommends including both a sequence and transcript identifier for some variants, with the transcript identifier in parentheses e.g.: https://hgvs-nomenclature.org/stable/recommendations/DNA/substitution/. A similar issue came up previously with regard to gene names (#257 ), but this seems to have better logic behind it, as the transcript identifier is less ambiguous, and is apparently required in some cases to make the variant description unambiguous

Describe the solution you'd like

Either:

  • allow hgvs's parser to parse variants that include a transcript identifier, even if the identifier is ignored.
  • parse the transcript identifier as well and store it in the resulting object

NB: please forgive my lack of knowledge on any of the above, I am more of a software developer than a bioinformatician.

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