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mRNA without gene #369

Merged
merged 4 commits into from
May 21, 2024
Merged

mRNA without gene #369

merged 4 commits into from
May 21, 2024

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MatBarba
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  • Add explicit support for mRNA (with exon and CDS) without a gene parent.
  • Also change the IDs in lone transcript cases: keep the ID on the transcript (and their children) and generate a new ID for the gene, namely the transcript ID + "_gene"
  • Also change the gene type to pseudogene if the CDS has a pseudo=true attribute
  • Update the tests accordingly

@MatBarba MatBarba self-assigned this May 21, 2024
@MatBarba
Revert, keep transcript ID as gene + bugfix
8be370e 
Easier to keep the "main" ID as gene

Also remove the Parent attribs from the exon and CDS to avoid a bug
where they get both the old and new Parent ID at the same time
JAlvarezJarreta
JAlvarezJarreta approved these changes May 21, 2024
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@JAlvarezJarreta JAlvarezJarreta left a comment

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Happy if CI/CD is happy. Weird bugs are always weird, no matter when.

@MatBarba MatBarba merged commit ed55f35 into main May 21, 2024
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@MatBarba MatBarba deleted the mbarba/lone_mrna branch May 21, 2024 14:33
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@JAlvarezJarreta JAlvarezJarreta JAlvarezJarreta approved these changes

@Dishalodha Dishalodha Awaiting requested review from Dishalodha

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@MatBarba @JAlvarezJarreta