From 34e2343e28d090a82c8d6a6b57b361aaf8d280a3 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Wed, 12 Jun 2019 15:38:02 -0400
Subject: [PATCH] fix
---
mhcflurry/class1_affinity_predictor.py | 16 ++++++++++++++--
mhcflurry/train_pan_allele_models_command.py | 2 +-
2 files changed, 15 insertions(+), 3 deletions(-)
diff --git a/mhcflurry/class1_affinity_predictor.py b/mhcflurry/class1_affinity_predictor.py
index 59e9b7ac..d6410b49 100644
--- a/mhcflurry/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_predictor.py
@@ -1032,8 +1032,20 @@ class Class1AffinityPredictor(object):
logging.warning(msg)
if throw:
raise ValueError(msg)
- mask = df.supported_peptide_length
- if mask.sum() > 0:
+ mask = df.supported_peptide_length & (
+ ~df.normalized_allele.isin(unsupported_alleles))
+ if mask is None or mask.all():
+ # Common case optimization
+ allele_encoding = AlleleEncoding(
+ df.normalized_allele,
+ borrow_from=master_allele_encoding)
+ for (i, model) in enumerate(self.class1_pan_allele_models):
+ predictions_array[:, i] = (
+ model.predict(
+ peptides,
+ allele_encoding=allele_encoding,
+ **model_kwargs))
+ elif mask.sum() > 0:
masked_allele_encoding = AlleleEncoding(
df.loc[mask].normalized_allele,
borrow_from=master_allele_encoding)
diff --git a/mhcflurry/train_pan_allele_models_command.py b/mhcflurry/train_pan_allele_models_command.py
index 2c16f263..88ca3e2a 100644
--- a/mhcflurry/train_pan_allele_models_command.py
+++ b/mhcflurry/train_pan_allele_models_command.py
@@ -417,7 +417,7 @@ def train_model(
save_to):
import keras.backend as K
- K.clear_session()
+ K.clear_session() # release memory
df = GLOBAL_DATA["train_data"]
folds_df = GLOBAL_DATA["folds_df"]
--
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