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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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infer quant --ref and --index #28

Closed kfuku52 closed 1 year ago

kfuku52 commented 3 years ago

As reference fasta should be identifiable from the input metadata table (by species name), we should support quant --ref "infer", which automatically detects the reference fasta in the default reference directory (I think we don't have such dir yet, so let's say amalgkit_out/reference/). File names should be like Arabidopsis_thaliana_ANYANNOTATIONHERE.fasta.gz. quant --index "infer" should also be supported similarly.

Hego-CCTB commented 3 years ago

Yeah, I thought about something like this. This would also tie in to a amalgkit sanity functionality we talked about in another thread.

kfuku52 commented 3 years ago

Will you work on this?

Hego-CCTB commented 3 years ago

Sure! I actually already have code for something very close to this.

Hego-CCTB commented 1 year ago

https://github.com/kfuku52/amalgkit/issues/33 and https://github.com/kfuku52/amalgkit/issues/72