This code is definitely out of date.

[Dr-Doomhammer]

Only Python 2.7 is acceptable.

[DininduSenanayake]

@Dr-Doomhammer We have had some trouble with getting this to work with Python 3. Then we came across this https://pypi.org/project/MicrobeCensus-SourceApp/ which is working perfectly fine with Python/3.11

I believe this was maintained by https://github.com/bglindner/SourceApp

[bglindner]

Hey, I'm the SourceApp developer and I forked MicrobeCensus to embed it within my tool. But you can install my fork directly from PyPI without using SourceApp (see the instructions on the repo linked above -- it's just a quick pip install). I traced MicrobeCensus' code and only a few lines needed to be updated for compatibility with modern Python. I make no guarantees I'll keep it working into the future!

It would definitely be nice to revisit "genome equivalents" now that we have a lot more genomes in public databases. Having a handy tool to get SCG coverage from a metagenome is so nice!

Edit just to add: the above is really only necessary if you're trying to install MicrobeCensus in an environment running modern python. You can easily still install the tool in a environment running python=2.7 and it will run perfectly fine. That's as simple as:

mamba create -n census python=2.7
mamba activate census
mamba install -c bioconda microbecensus=1.1.1
run_microbe_census.py -h