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bvalot / pyMLST

whole genome MLST analysis
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biopython deprecation warning #23

Closed ammaraziz closed 6 months ago

ammaraziz commented 7 months ago

Hi,

Thanks for creating pyMLSt

I installed the tool via conda.

Details:

Command I ran:

claMLST 
claMLST create
etc

I get this warning:

python3.10/site-packages/Bio/Application/__init__.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.

Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.

We instead now recommend building your command line and invoking it directly
with the subprocess module.
  warnings.warn(
bvalot commented 7 months ago

Thank you for this advice. I use this module for performing global alignment using MAFFT. I would use direct command line instead.

I would change this part in the next release. Normally, you can always run pyMLST.