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cgat-developers / cgat-flow

cgat-flow repository
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GREAT regions #103

Closed IanSudbery closed 4 years ago

IanSudbery commented 5 years ago

The docs for pipeline_genesets states that it generates GREAT regions, but I can't find any task that actaully does that in the pipeline.

Acribbs commented 5 years ago

Ah I remember having this team discussion, we decided to remove it from the pipeline because the latest genome builds weren't supported.

If you would like to re-implement the function it is in the old annotations pipeline (https://github.com/CGATOxford/CGATPipelines/blob/015dba9ca099c3bf959774498453e8b77ef8e3b5/CGATPipelines/pipeline_annotations.py). I can remove the reference to GREAT in the docs

IanSudbery commented 5 years ago

I'm sure we are fine if we just update the docs. The functionality is still there in gff2gff.

How come the latest genome builds aren't supported, I thought it was just a case of finding the mid-point between genes?

Acribbs commented 5 years ago

I think it was something to do with gene biotypes changing in latest builds but I cant really remember now.

Acribbs commented 4 years ago

closing because I have removed from docs: 92aeb2052f6391684f54997caf927b9c7fb1f586