Phenotrex installation help

Question

[sagrant]

Hi, I'm a bit of a bioinformatics newbie and I've been trying to find a program that can predict microbial phenotypes based on their genome sequence. I found a program called phenotrex but I am having a hard time installing all the dependencies.

When I run the command:

phenotrex compute-genotype --out Pse_aerug Pseudomonas_aeruginosa.fna

It spits out the error:

ModuleNotFoundError: No module named 'deepnog.models.deepencoding'

When I manually check what's going on in the package dependencies folder, I don't see a "deepencoding" module under the models module, so I have a feeling that the program wasn't installed correctly. Does anyone have any advice for how to proceed? Alternatively, does anyone know of a different program that will help me analyze characteristics of microbes based on (preferably) FASTA files pulled off the internet?

Thanks!

Answer 1

[vimalkvn]

Looks like the deepencoding module has been renamed in deepnog v1.2.3.

Possible solutions (Note: I haven't tested this!)

If you installed phenotrex using pip, you can try installing an earlier version of deepnog using:

pip install deepnog==1.2.2

Alternatively, you can try installing the latest version of phenotrex from their GitHub repository. Related documentation.

[sagrant]

This fixed it! Thank you so much!