if float(strain_vals.count("1"))/float(len(strain_vals)) > t:
with the documentation for --threshold: "proportion of strains to be considered an ortholog".
Should that be ">" or ">="?
I would prefer ">=" so that "--threshold 1.0" is equivalent to not specifying "--threshold" at all, but I realize that would introduce an incompatibility. So, perhaps the documentation could be clarified that the threshold is "strictly greater than"?
Compare line 59 of
IdentifyOrthologs.py:with the documentation for
--threshold: "proportion of strains to be considered an ortholog".Should that be ">" or ">="?
I would prefer ">=" so that "--threshold 1.0" is equivalent to not specifying "--threshold" at all, but I realize that would introduce an incompatibility. So, perhaps the documentation could be clarified that the threshold is "strictly greater than"?
Thank you for your consideration.