From 333cfb38d0487d75ad28a71482b9da0c38a32ac2 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 27 Jan 2020 11:31:18 -0500
Subject: [PATCH] fix
---
downloads-generation/data_evaluation/GENERATE.sh | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/downloads-generation/data_evaluation/GENERATE.sh b/downloads-generation/data_evaluation/GENERATE.sh
index 569db7ad..31f97353 100755
--- a/downloads-generation/data_evaluation/GENERATE.sh
+++ b/downloads-generation/data_evaluation/GENERATE.sh
@@ -63,7 +63,7 @@ else
time python make_benchmark.py \
--hits "$(pwd)/hits_with_tpm.csv.bz2" \
--proteome-peptides "$(mhcflurry-downloads path data_mass_spec_benchmark)/proteome_peptides.all.csv.bz2" \
- --decoys-per-hit 99 \
+ --decoys-per-hit 110 \
--exclude-train-data "$(mhcflurry-downloads path models_class1_pan_variants)/models.no_additional_ms/train_data.csv.bz2" \
--only-format MONOALLELIC \
--out "$(pwd)/benchmark.monoallelic.csv"
@@ -80,7 +80,7 @@ else
--hits "$(pwd)/hits_with_tpm.csv.bz2" \
--proteome-peptides "$(mhcflurry-downloads path data_mass_spec_benchmark)/proteome_peptides.all.csv.bz2" \
--exclude-train-data "$(mhcflurry-downloads path models_class1_pan)/models.combined/train_data.csv.bz2" \
- --decoys-per-hit 99 \
+ --decoys-per-hit 110 \
--only-format MULTIALLELIC \
--out "$(pwd)/benchmark.multiallelic.csv"
bzip2 -f benchmark.multiallelic.csv
@@ -101,13 +101,12 @@ else
--models \""$(mhcflurry-downloads path models_class1_pan_variants)/models.no_additional_ms"\" \
--affinity-only \
--no-affinity-percentile \
- --out "$(pwd)/benchmark.monoallelic.predictions.csv" \
+ --out "$(pwd)/benchmark.monoallelic.no_additional_ms.csv" \
--no-throw >> commands/monoallelic.sh
echo bzip2 -f "$(pwd)/benchmark.monoallelic.predictions.csv" >> commands/monoallelic.sh
fi
-
### AFFINITY PREDICTORS: MULTIALLELIC
if [ "$2" == "continue-incomplete" ] && [ -f "benchmark.multiallelic.production.csv.bz2" ]
then
--
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