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bioforensics / yeat

YEAT: Your Everyday Assembly Tool
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Adding FASTQC Support #5

Closed danejo3 closed 2 years ago

danejo3 commented 2 years ago

The purpose of this PR is to resolve #4.

FastQC is a tool used to provide an overview of basic quality control metrics for raw next-generation sequencing data.

In this new PR, reads will be executed with the fastqc command. The fastqc HTML results will be found in the seq/fastqc directory.

danejo3 commented 2 years ago

I haven't been able to figure out how to remove this warning. This warning is also seen in mystt as well when you run the tests.

It seems like the deprecation warning is coming from a library that python uses within itself. I am using python 3.9.7.

I found a thread of someone pointing this out and creating a PR for it. (Not sure what rabbit hole I went down into...)

https://github.com/RazerM/ratelimiter/issues/10

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standage commented 2 years ago

I've seen it as well. Deprecation means that a language feature is slated for removal, but hasn't actually been removed yet. A kind of grace period during which packages have time to update the offending behavior. In both cases, the culprit code is in third-party libraries, so there's not much we can do except hope that the libraries are updated before the warnings become errors in the future.

danejo3 commented 2 years ago

@standage I think I've added everything for fastqc report. Let me know if you have any questions, thoughts, or concerns with this PR.

standage commented 2 years ago

A non-dry-run test of the "Animal" data bundled with YEAT was successful.

danejo3 commented 2 years ago

Thanks for the comments. Added everything that was suggested.