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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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redundant codes in quant #78

Closed kfuku52 closed 1 year ago

kfuku52 commented 2 years ago

load_metadata(args) takes care of --batch (and probably should do so too to --id), so I'm not sure if these three branch conditions are really necessary. @Hego-CCTB What do you think?

https://github.com/kfuku52/amalgkit/blob/9698f58f4def61cdff9cb1f3e9388132ed9594e6/amalgkit/quant.py#L150-L179

Hego-CCTB commented 2 years ago

--batch is something I have barely touched so far, so I'm unsure if I can make a good decision on this. That's why --batch is isolated this way. How does load_metadata interact with batch?

kfuku52 commented 2 years ago

OK, you should have a debug setting for your test data with --batch option. With --batch, amalgkit getfastq/quant handles only one sample (one row in the metadata). load_metadata should return single-row metadata with --batch. So the three branch conditions wouldn't be necessary. Could you set up a debug setting with --batch and remove the branch conditions if no bad effect?

Hego-CCTB commented 2 years ago

Sure!

Hego-CCTB commented 2 years ago

Did some testing and, yes, this codeblock can be safely removed!

My PyCharm is currently having issues with Git, but I'll push an update as soon as I figure that one out.

Hego-CCTB commented 1 year ago

Never came back to close this. That code has been removed.