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linsalrob / PhiSpy

Prediction of prophages from bacterial genomes
MIT License
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Impossible to use training sets kept in other location than INSTALLATION_DIR #31

Open pdec opened 4 years ago

pdec commented 4 years ago

I noticed that the below check forces users to keep their retrained reference datasets in INSTALLATION_DIR/PhiSpyModules/data directory https://github.com/linsalrob/PhiSpy/blob/540fbf2548cd6580a6fd9d0a8e003226b1044710/PhiSpyModules/classification.py#L34-L36

The same will happen with kmers file within makeTest.py and makeTrain.py https://github.com/linsalrob/PhiSpy/blob/540fbf2548cd6580a6fd9d0a8e003226b1044710/PhiSpyModules/makeTest.py#L16-L20

Hence, while retraining one needs to point the PhiSpy's installation dir (e.g. /usr/local/lib/python3.6/site-packages/PhiSpy...) and can't keep separate trainSets dirs.

linsalrob commented 4 years ago

I agree with this issue, but will not refactor the code for the current release. We will work on this for the next release.