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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 · 0 comments
Open

let user use genomic accession as reference for coordinates #327

katiestahl opened this issue Sep 5, 2024 · 0 comments
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enhancement New feature or request help wanted Extra attention is needed priority:low Low priority 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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Labels
enhancement New feature or request help wanted Extra attention is needed priority:low Low priority ux
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