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which() function needs to call os.path.basename

Hey,

I was trying to run your pipeline on the test dataset and it got hung up trying to verify the location and executability of the other scripts packaged with this repo. The which() function in Phylogeny/bin/makephylogenysh.py fails when the input executable name is prefixed with a relative path (e.g., ../Phylogeny/bin/allgenesingb.py) and returns None. I extracted the function and put it in its own script to test.

bredeson|21:57:42|workdir> cat which.py 
import os
import sys

def which(pgm):
    path=os.getenv('PATH')
    for p in path.split(os.path.pathsep):
        p=os.path.join(p,pgm)
        if os.path.exists(p) and os.access(p,os.X_OK):
            return p


print(which(sys.argv[1]))

bredeson|22:23:25|workdir> python ./which.py ../Phylogeny/bin/allgenesingb.py
None
bredeson|22:23:37|workdir> python ./which.py allgenesingb.py
/path/to/Phylogeny/bin/allgenesingb.py
bredeson|22:23:45|workdir> python ./which.py /path/to/Phylogeny/bin/allgenesingb.py
/path/to/Phylogeny/bin/allgenesingb.py

Hope this helps!

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