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Also accept "region" as synonym of "source" for gb files? #1643

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corneliusroemer opened this issue Sep 25, 2024 · 1 comment
Open

Also accept "region" as synonym of "source" for gb files? #1643

corneliusroemer opened this issue Sep 25, 2024 · 1 comment
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enhancement New feature or request

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@corneliusroemer
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Context

I've been hitting a bug with Augur >=24 on a preexisting workflow that used a genbank file that uses "region" in place of "source".

This PR started requiring specifically source: #1351 - and I never traced down while I got the failure. I didn't understand at first what was happening. In retrospect it would have been helpful to have the error mention that this breaking change occurs since v24

Description

I don't know much about genbank files in the wild, so maybe this usage of region instead of source was an idiosyncracy of my gb file (I don't know where I got it from) - but in case that others use region instead of source, it might make sense to treat region as a synonym of source? At least in my case, the two contain equivalent information:

@corneliusroemer corneliusroemer added the enhancement New feature or request label Sep 25, 2024
@jameshadfield
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In retrospect it would have been helpful to have the error mention that this breaking change occurs since v24

Do you mean the error thrown at runtime? The changelog mentioned this as a major change:

ancestral, translate: GenBank files now require the (GFF mandatory) source feature to be present.[#1351][] (@jameshadfield)

GFFs are rather varied in the wild - I tried to add in helpful runtime errors when unexpected cases are encountered, but we could always do with more!

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