quant overhaul - Githubissues

kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics

BSD 3-Clause "New" or "Revised" License

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quant overhaul #40

Closed Hego-CCTB closed 3 years ago

Hego-CCTB commented 3 years ago

While fixing some minor bugs in quant, it became clear that quant needs some love.

obsolete --build_index
make metadata a required input
read library type(single/paired end) and fragment length directly from the local metadata, instead of querying SRA again.
the way kallisto is called currently makes it harder to implement alternative quantification programs (such as salmon)
theoretically, the mapping rate can be directly taken from the kallisto output

@kfuku52 what's your opinion on this?

kfuku52 commented 3 years ago

Agreed except

the way kallisto is called currently makes it harder to implement alternative quantification programs (such as salmon)

I've never used salmon but wouldn't it be easy to introduce a new option like amalgkit quant --mapper "salmon" and change the behavior accordingly? I expect some reformatting is needed afterward but that wouldn't be fundamentally difficult.

Hego-CCTB commented 3 years ago

What I was thinking of, was to put all kallisto related code into a function like run_kallisto() and make a separate function for alternatives, since input/output formats may vary.

kfuku52 commented 3 years ago

That's what we do! Please go ahead with it. Improving modularity is one of the things we have to do routinely.

Hego-CCTB commented 3 years ago

--build_index is now obsolete
--ref is now replaced by --index
metadata is now a required input
library type and fragment length are now read out from the metadata directly
removed unused dependencies
restructured code to modularize kallisto call

https://github.com/kfuku52/amalgkit/commit/2052d6f5475f10ea0f69adcecd408db4d99b9f25