A question about the '--threshold-affinity' parameter

[chenli-bioinfo]

Dear author,

I was running mhcflurry using:

mhcflurry-predict-scan test.fasta --peptide-lengths 8-11 --alleles HLA-A0101 --threshold-affinity 500 --threshold-affinity-percentile 2.0 --out ./test.csv

While the percentile threshold was correctly applied, I found that affinity seemed not to be cut off:

I was therefore wondering if I was understanding the parameters correctly.

Thank you very much.

Chen

[timodonnell]

Thanks for reporting this, Chen. This is happening because only one quantity can be filtered, so your affinity threshold is being ignored. The library API (Class1PresentationPredictor.predict_sequences) makes this clear but I agree in the commandline tool this is super confusing. I am changing this now to have different semantics for the commandline tool and to apply all the filters you specify. The fix will go into the next release.