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Linker is not a region_type #14

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emattei opened this issue Jun 8, 2023 · 1 comment
Closed

Linker is not a region_type #14

emattei opened this issue Jun 8, 2023 · 1 comment

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@emattei
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emattei commented Jun 8, 2023

In the example specs there is a region_type called linker1
https://github.com/IGVF/seqspec/blob/0d408a38cec4e632f85a20bd95c26c56ad1ac1dc/specs/SHARE-seq/spec.yaml#LL457C1-L457C1

But it doesn't seem to be an allowed type https://github.com/IGVF/seqspec/blob/main/docs/SPECIFICATION.md

What is the correct type to use.

Moreover, region_type has a number to it but I assume that that spec it is outdated and it should be region_type: linker and region_id: linker-1

@sbooeshaghi
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You're right- that is not an allowed region_type. I've updated the seqspec schema so that seqspec check will validate region_type and sequence_type against a controlled vocabulary so the tool will now catch bugs like this.

And yes- your suggested change is the right one. I've updated the spec you've referenced in the repo. Thank you!

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