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Support transcript identifiers (in parentheses) in variants #735

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marius-mather opened this issue Apr 10, 2024 · 1 comment
Open

Support transcript identifiers (in parentheses) in variants #735

marius-mather opened this issue Apr 10, 2024 · 1 comment
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keep alive exempt issue from staleness checks

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@marius-mather
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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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This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 7 days.

@github-actions github-actions bot added the stale Issue is stale and subject to automatic closing label Jul 11, 2024
@jsstevenson jsstevenson added keep alive exempt issue from staleness checks and removed stale Issue is stale and subject to automatic closing labels Jul 11, 2024
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