From 9361bda1b04aeec7af3a9cc9ee48dc97f25aa137 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 16 Sep 2019 15:34:38 -0400
Subject: [PATCH] fix
---
.../models_class1_pan/GENERATE.WITH_HPC_CLUSTER.sh | 4 ++--
downloads-generation/models_class1_pan/GENERATE.sh | 4 ++--
mhcflurry/class1_neural_network.py | 11 +++++++----
3 files changed, 11 insertions(+), 8 deletions(-)
diff --git a/downloads-generation/models_class1_pan/GENERATE.WITH_HPC_CLUSTER.sh b/downloads-generation/models_class1_pan/GENERATE.WITH_HPC_CLUSTER.sh
index 5d21a2e6..807770e6 100755
--- a/downloads-generation/models_class1_pan/GENERATE.WITH_HPC_CLUSTER.sh
+++ b/downloads-generation/models_class1_pan/GENERATE.WITH_HPC_CLUSTER.sh
@@ -58,8 +58,8 @@ do
--data "$MODELS_DIR/train_data.csv.bz2" \
--models-dir "$MODELS_DIR" \
--out-models-dir models.${kind} \
- --min-models 8 \
- --max-models 32 \
+ --min-models 2 \
+ --max-models 8 \
--num-jobs $NUM_JOBS --max-tasks-per-worker 1 --gpus $GPUS --max-workers-per-gpu 1
cp "$MODELS_DIR/train_data.csv.bz2" "models.${kind}/"
diff --git a/downloads-generation/models_class1_pan/GENERATE.sh b/downloads-generation/models_class1_pan/GENERATE.sh
index a0842d31..9b4e07b4 100755
--- a/downloads-generation/models_class1_pan/GENERATE.sh
+++ b/downloads-generation/models_class1_pan/GENERATE.sh
@@ -50,8 +50,8 @@ do
--data "$MODELS_DIR/train_data.csv.bz2" \
--models-dir "$MODELS_DIR" \
--out-models-dir models.${kind} \
- --min-models 8 \
- --max-models 32 \
+ --min-models 2 \
+ --max-models 8 \
--num-jobs 0 \
--num-jobs $NUM_JOBS --max-tasks-per-worker 1 --gpus $GPUS --max-workers-per-gpu 1
diff --git a/mhcflurry/class1_neural_network.py b/mhcflurry/class1_neural_network.py
index dd367a33..33709f04 100644
--- a/mhcflurry/class1_neural_network.py
+++ b/mhcflurry/class1_neural_network.py
@@ -769,9 +769,11 @@ class Class1NeuralNetwork(object):
total_random_peptides_per_length += num_per_length
allele_to_num_per_length[allele] = num_per_length
- for _ in random_negative_lengths:
- for (allele, num) in allele_to_num_per_length.items():
- random_negative_alleles.append([allele] * num)
+ if allele_encoding is not None:
+ random_negative_alleles = []
+ for _ in random_negative_lengths:
+ for (allele, num) in allele_to_num_per_length.items():
+ random_negative_alleles.append([allele] * num)
numpy.testing.assert_equal(
len(random_negative_alleles),
@@ -789,7 +791,8 @@ class Class1NeuralNetwork(object):
total_random_peptides_per_length,
length=length,
distribution=aa_distribution))
- # important NOT to shuffle peptides.
+ # important NOT to shuffle peptides, since they correspond with
+ # specific alleles.
return EncodableSequences.create(peptides)
else:
raise NotImplementedError(
--
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