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let user use genomic accession as reference for coordinates #327

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katiestahl opened this issue Sep 5, 2024 · 1 comment
Open

let user use genomic accession as reference for coordinates #327

katiestahl opened this issue Sep 5, 2024 · 1 comment
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enhancement New feature or request help wanted Extra attention is needed priority:low Low priority stale ux

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@katiestahl
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  • General complicating factor: the gene/genomic accession/transcript accession are basically used as "guides" to figure out where the numeric coordinates given should be positioned. In general, chromosome/genomic accession is ignored if a transcript is given. But if a user wants to use the genomic accession as the reference for the genomic coordinates, they need a way of picking a genomic accession manually or from a list of options, and to leave the transcript field blank, because Cool-Seq-Tool will always prefer a transcript over a genomic accession if both are given.
    • Therefore, I think we need a way to specify genomic accession or produce a dropdown of accessions from the entered gene (see eg (ELN, NC_000007.13, 73442503:73457929) gives incorrect ending coordinate error #277 for why) and/or leave transcript blank optionally
    • To the extent ^^^ that the chromosome field is now locked down, we can probably also revisit whether it still needs the annoying hover-over that clarifies the kinds of legal inputs.

Originally posted by @jsstevenson in #273 (review)

@katiestahl katiestahl added enhancement New feature or request help wanted Extra attention is needed ux priority:low Low priority labels Sep 5, 2024
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github-actions bot commented Mar 5, 2025

This issue is stale because it has been open 180 days with no activity. This issue will be closed if no further activity occurs in 14 days.

@github-actions github-actions bot added the stale label Mar 5, 2025
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Labels
enhancement New feature or request help wanted Extra attention is needed priority:low Low priority stale ux
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