From 67df0dac805f746148bcb0b81a9690aeb4d54571 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sat, 25 Jan 2020 17:39:35 -0500
Subject: [PATCH] fixes
---
.../GENERATE.WITH_HPC_CLUSTER.sh | 1 -
.../data_evaluation/GENERATE.sh | 59 +++++++++++++------
.../data_evaluation/predict.py | 0
3 files changed, 40 insertions(+), 20 deletions(-)
delete mode 100755 downloads-generation/data_evaluation/GENERATE.WITH_HPC_CLUSTER.sh
delete mode 100644 downloads-generation/data_evaluation/predict.py
diff --git a/downloads-generation/data_evaluation/GENERATE.WITH_HPC_CLUSTER.sh b/downloads-generation/data_evaluation/GENERATE.WITH_HPC_CLUSTER.sh
deleted file mode 100755
index 53125eb7..00000000
--- a/downloads-generation/data_evaluation/GENERATE.WITH_HPC_CLUSTER.sh
+++ /dev/null
@@ -1 +0,0 @@
-bash GENERATE.sh cluster
diff --git a/downloads-generation/data_evaluation/GENERATE.sh b/downloads-generation/data_evaluation/GENERATE.sh
index 2d904d9a..9a8c336e 100755
--- a/downloads-generation/data_evaluation/GENERATE.sh
+++ b/downloads-generation/data_evaluation/GENERATE.sh
@@ -96,8 +96,10 @@ else
time mhcflurry-predict \
benchmark.monoallelic.csv.bz2 \
--allele-column hla \
- --prediction-column-prefix prediction.no_additional_ms \
+ --prediction-column-prefix no_additional_ms_ \
--models "$(mhcflurry-downloads path models_class1_pan_variants)/models.no_additional_ms" \
+ --affinity-only \
+ --no-affinity-percentile \
--out benchmark.monoallelic.predictions.csv \
--no-throw
bzip2 -f benchmark.monoallelic.predictions.csv
@@ -126,27 +128,45 @@ then
echo "Reusing existing multiallelic predictions"
else
cp $SCRIPT_DIR/predict.py .
- time python predict.py \
- benchmark.multiallelic.csv \
- --models \
- "$(mhcflurry-downloads path models_class1_pan)/models.combined" \
- "$(mhcflurry-downloads path models_class1_pan_variants)/models.*" \
- --out "$(pwd)/benchmark.multiallelic.predictions.csv"
+ time mhcflurry-predict \
+ benchmark.multiallelic.csv.bz2 \
+ --allele-column hla \
+ --prediction-column-prefix mhcflurry_production_ \
+ --models "$(mhcflurry-downloads path models_class1_pan)/models.combined" \
+ --affinity-only \
+ --no-affinity-percentile \
+ --out "$(pwd)/benchmark.multiallelic.predictions1.csv"
+
+ for variant in no_additional_ms compact_peptide affinity_only no_pretrain single_hidden_no_pretrain
+ do
+ time mhcflurry-predict \
+ "$(pwd)/benchmark.multiallelic.predictions1.csv" \
+ --allele-column hla \
+ --prediction-column-prefix "${variant}_" \
+ --models "$(mhcflurry-downloads path models_class1_pan_variants)/models.$variant" \
+ --affinity-only \
+ --no-affinity-percentile \
+ --out "$(pwd)/benchmark.multiallelic.predictions1.csv"
+ done
+
bzip2 -f benchmark.multiallelic.predictions1.csv
rm -f benchmark.multiallelic.predictions2.csv.bz2
fi
+
### PRESENTATION: WITH FLANKS
if [ "$2" == "continue-incomplete" ] && [ -f "benchmark.multiallelic.predictions2.csv.bz2" ]
then
echo "Reusing existing multiallelic predictions2"
else
- mhcflurry-predict-presentation \
- "$(pwd)/benchmark.multiallelic.predictions1.csv" \
- --out "$(pwd)/benchmark.multiallelic.predictions2.csv" \
+ time mhcflurry-predict \
+ "$(pwd)/benchmark.multiallelic.predictions1.csv.bz2" \
+ --allele-column hla \
+ --prediction-column-prefix presentation_with_flanks_ \
--models "$(mhcflurry-downloads path models_class1_presentation)/models" \
- --include-details \
- --prediction-col presentation_with_flanks \
+ --no-affinity-percentile \
+ --out "$(pwd)/benchmark.multiallelic.predictions2.csv"
+
bzip2 -f benchmark.multiallelic.predictions2.csv
rm -f benchmark.multiallelic.predictions3.csv.bz2
fi
@@ -156,18 +176,19 @@ if [ "$2" == "continue-incomplete" ] && [ -f "benchmark.multiallelic.predictions
then
echo "Reusing existing multiallelic predictions3"
else
- mhcflurry-predict-presentation \
- "$(pwd)/benchmark.multiallelic.predictions2.csv" \
- --out "$(pwd)/benchmark.multiallelic.predictions3.csv" \
+ time mhcflurry-predict \
+ "$(pwd)/benchmark.multiallelic.predictions2.csv.bz2" \
+ --allele-column hla \
+ --prediction-column-prefix presentation_with_flanks_ \
--models "$(mhcflurry-downloads path models_class1_presentation)/models" \
- --include-details \
- --prediction-col presentation_without_flanks \
- --no-flanks
+ --no-affinity-percentile \
+ --no-flanking \
+ --out "$(pwd)/benchmark.multiallelic.predictions3.csv"
+
bzip2 -f benchmark.multiallelic.predictions3.csv
fi
-
cp $SCRIPT_ABSOLUTE_PATH .
bzip2 -f "$LOG"
for i in $(ls LOG-worker.*.txt) ; do bzip2 -f $i ; done
diff --git a/downloads-generation/data_evaluation/predict.py b/downloads-generation/data_evaluation/predict.py
deleted file mode 100644
index e69de29b..00000000
--
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