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Currently necessary to run HostG from within the HostG directory? #2
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Ummm. Yes, currently the CNN model can only be run in the given model because the path of the CNN script is hardcoded. If you are using an HPC, you can sbatch your job under the HostG folder. That will work. Best, |
Hi Jiayu, Thanks for the quick reply. Ok, I'll continue running from within the I had a quick look at if I could patch this quickly for our system, but as there's a number of subscripts with the
Thanks again for the reply. I had a quick follow up question regarding outputting the threshold scores, but I will open a new thread for that one. Kind regards, |
Hi there,
Thanks for your work on HostG. It looks like a great tool, and I'm keen to give it a test run with some current data we're working on.
I just wanted to check if I'm missing something, but from what I can tell, is it currently necessary to run the tool from within the
HostG/
directory?I.e. The current calls to other python scripts in the format
cmd = "python run_CNN.py"
appear to only look within the working directory forrun_CNN.py
even ifHostG/
is added to$PATH
. Similarly, the call to the database (dataset/
) appears to be hardcoded as being within the current directory (e.g. withinrun_KnowledgeGraph.py
:pkl.load(open("dataset/phage2id.dict",'rb'))
).Thanks again for all your work on this, and I'm looking forward to seeing how the outputs from our data look.
Kind regards,
Mike.
(p.s. I installed simply by cloning the repo rather than via anaconda, but perhaps it was written with the assumption that it only be run from directly within the conda environment?)
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