From b9dbc5beb5b4410043803aa2669d1b74c7149536 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 30 Sep 2019 21:25:52 -0400
Subject: [PATCH] fix
---
.../data_mass_spec_benchmark/run_mhcflurry.py | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/downloads-generation/data_mass_spec_benchmark/run_mhcflurry.py b/downloads-generation/data_mass_spec_benchmark/run_mhcflurry.py
index e6ed769b..8eeb45f2 100644
--- a/downloads-generation/data_mass_spec_benchmark/run_mhcflurry.py
+++ b/downloads-generation/data_mass_spec_benchmark/run_mhcflurry.py
@@ -106,7 +106,11 @@ def run(argv=sys.argv[1:]):
alleles = [normalize_allele_name(a) for a in args.allele]
alleles = sorted(set(alleles))
- peptides = pandas.read_csv(args.input_peptides).peptide.unique()
+ peptides = pandas.read_csv(args.input_peptides).peptide.drop_duplicates()
+ print("Filtering to valid peptides. Starting at: ", len(peptides))
+ peptides = peptides[peptides.str.match("[ACDEFGHIKLMNPQRSTVWY]+")]
+ print("Filtered to: ", len(peptides))
+ peptides = peptides.unique()
num_peptides = len(peptides)
print("Predictions for %d alleles x %d peptides." % (
@@ -137,7 +141,7 @@ def run(argv=sys.argv[1:]):
GLOBAL_DATA["args"] = {
'verbose': args.verbosity > 0,
'model_kwargs': {
- 'batch_size': args.prediction_batch_size,
+ 'batch_size': args.batch_size,
}
}
@@ -239,7 +243,6 @@ def predict_for_allele(
predictions = predictor.predict(
peptides=chunk_peptides,
allele=allele,
- verbose=verbose,
throw=False,
model_kwargs=model_kwargs).astype('float32')
if verbose:
--
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