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marvel's Introduction

I am a Bioinformatician located in the Netherlands.

🛠️ Languages, tools, technologies

Python  Bash  Vim  Git  Jupyter  Docker

marvel's People

Contributors

deyvidamgarten avatar maitai avatar wwood avatar

marvel's Issues

Remove empty fastas from prokka before hmmsearching

If the input is large enough to be processed, but does not produce a valid fasta file (i.e. empty), hmm fails. It would be nice to keep going and analyze all other bins/contigs that do have some proteins predicted.

Possible fix:
remove all prokka dirs that have an empty fasta file. Then these are input to hmm and everyone is happy.

marvel ModuleNotFoundError: No module named 'sklearn.ensemble.forest'

According to this, with newer versions of scikit-learn the forest module has been renamed to sklearn.ensemble._forest.

So, create a fresh environment with

$ conda create -n marvel hmmer prokka numpy scipy biopython=1.75 scikit-learn=0.21.3

Same goes for biopython, I was getting some AlignIO related error. Once rolling back to 1.75 it was fixed.

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