From aba7f4df3073b4aab9eff8a1613f5ec1a081689f Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sat, 25 Jan 2020 11:53:52 -0500
Subject: [PATCH] fix
---
.../models_class1_presentation/GENERATE.sh | 17 +++++++++++------
1 file changed, 11 insertions(+), 6 deletions(-)
diff --git a/downloads-generation/models_class1_presentation/GENERATE.sh b/downloads-generation/models_class1_presentation/GENERATE.sh
index d528bb0a..c1086eb1 100755
--- a/downloads-generation/models_class1_presentation/GENERATE.sh
+++ b/downloads-generation/models_class1_presentation/GENERATE.sh
@@ -87,12 +87,17 @@ else
bzip2 -f train_data.csv
fi
-mhcflurry-class1-train-presentation-models \
- --data "$(pwd)/train_data.csv.bz2" \
- --affinity-predictor "$(mhcflurry-downloads path models_class1_pan)/models.combined" \
- --cleavage-predictor-with-flanks "$(mhcflurry-downloads path models_class1_cleavage)/models" \
- --cleavage-predictor-without-flanks "$(mhcflurry-downloads path models_class1_cleavage_variants)/models.selected.no_flank" \
- --out-models-dir "$(pwd)/models"
+if [ "$2" == "continue-incomplete" ] && [ -f "models/weights.csv" ]
+then
+ echo "Reusing existing trained predictor"
+else
+ mhcflurry-class1-train-presentation-models \
+ --data "$(pwd)/train_data.csv.bz2" \
+ --affinity-predictor "$(mhcflurry-downloads path models_class1_pan)/models.combined" \
+ --cleavage-predictor-with-flanks "$(mhcflurry-downloads path models_class1_cleavage)/models" \
+ --cleavage-predictor-without-flanks "$(mhcflurry-downloads path models_class1_cleavage_variants)/models.selected.no_flank" \
+ --out-models-dir "$(pwd)/models"
+fi
cp "$(mhcflurry-downloads path models_class1_pan)/models.combined/train_data.csv.bz2" models/affinity_predictor_train_data.csv.bz2
cp "$(mhcflurry-downloads path models_class1_cleavage)/models/train_data.csv.bz2" models/cleavage_predictor_train_data.csv.bz2
--
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