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mgtools / MinPath

MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.
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Add "mpsfile" parameter to help text and fix remove command #2

Open pooranis opened 3 years ago

pooranis commented 3 years ago

Hello! MinPath.py has facility to accept -mps mpsfile command line option, so I've included it in the help text. Additionally, all code in the script uses the mpsfile variable except at the very end, when the temporary mps file is removed - it is hardcoded as test.mps, so I've changed it to use the variable. I find this option helpful, as I often run MinPath in parallel on different sample annotations in a dataset, and specifying a unique per-sample temp filename helps avoid overwriting, etc. Hopefully, you can accept or modify these changes.

Thanks for your very useful tool!

khemlalnirmalkar commented 3 years ago

Hi, please can you help with this error, got using MinPath

now write mps file.. End of PrintMPS now run command = /scratch/knirmalk/dbs/geneQuantDBs/MinPath/glpk-4.6/examples/glpsol test.mps -o test.mps.LPout open file test.mps.LPout error

Thanks