From 2991a93ad3016f661e319faa6a10620e45df0631 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 3 Jan 2020 16:33:31 -0500
Subject: [PATCH] fix
---
.../run_predictors.py | 27 +++++++++++++++++--
1 file changed, 25 insertions(+), 2 deletions(-)
diff --git a/downloads-generation/data_mass_spec_benchmark/run_predictors.py b/downloads-generation/data_mass_spec_benchmark/run_predictors.py
index 14916c45..5bdd02db 100644
--- a/downloads-generation/data_mass_spec_benchmark/run_predictors.py
+++ b/downloads-generation/data_mass_spec_benchmark/run_predictors.py
@@ -394,8 +394,31 @@ def do_predictions_mhctools(work_item_dicts, constant_data=None):
program_name="netMHCpan-4.0",
mode="elution_score")
elif predictor_name == "mixmhcpred":
- predictor = mhctools.MixMHCpred(
- alleles=alleles)
+ # Empirically determine supported alleles.
+ mixmhcpred_usable_alleles = []
+ unusable_alleles = []
+ for allele in alleles:
+ predictor = mhctools.MixMHCpred(alleles=[allele])
+
+ # We use inf not nan to indicate unsupported alleles since
+ # we use nan to indicate incomplete results that still need
+ # to execute.
+ empty_results = pandas.Series(index=peptides,
+ dtype=numpy.float16)
+ empty_results[:] = numpy.inf
+ try:
+ predictor.predict_peptides_dataframe(["PEPTIDESS"])
+ mixmhcpred_usable_alleles.append(allele)
+ except ValueError:
+ unusable_alleles.append(allele)
+ for col in cols:
+ result["%s %s" % (allele, col)] = empty_results.values
+
+ print("MixMHCpred usable alleles: ", *mixmhcpred_usable_alleles)
+ print("MixMHCpred unusable alleles: ", *unusable_alleles)
+ predictor = mhctools.MixMHCpred(alleles=alleles)
+ assert mixmhcpred_usable_alleles, mixmhcpred_usable_alleles
+ alleles = mixmhcpred_usable_alleles
else:
raise ValueError("Unsupported", predictor_name)
--
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