From a4b7e0c68120576f854d716c166f76eeda271f10 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 6 Mar 2020 09:46:24 -0500
Subject: [PATCH] add variant
---
.../models_class1_pan_variants/GENERATE.sh | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/downloads-generation/models_class1_pan_variants/GENERATE.sh b/downloads-generation/models_class1_pan_variants/GENERATE.sh
index 7195099c..e36df1d7 100755
--- a/downloads-generation/models_class1_pan_variants/GENERATE.sh
+++ b/downloads-generation/models_class1_pan_variants/GENERATE.sh
@@ -69,7 +69,7 @@ then
python generate_hyperparameters.py hyperparameters.production.yaml compact_peptide > hyperparameters.compact_peptide.yaml
fi
-VARIANTS=( no_additional_ms_ms_only_0nm ms_only_0nm no_additional_ms_0nm 0nm no_additional_ms no_pretrain compact_peptide 34mer_sequence single_hidden_no_pretrain affinity_only )
+VARIANTS=( no_additional_ms_ms_only_0nm ms_only_0nm no_additional_ms_0nm 0nm 500nm no_additional_ms no_pretrain compact_peptide 34mer_sequence single_hidden_no_pretrain affinity_only )
for kind in "${VARIANTS[@]}"
do
@@ -127,6 +127,16 @@ do
HYPERPARAMETERS=hyperparameters.production.yaml
fi
+ if [ "$kind" == "500nm" ]
+ then
+ TRAINING_DATA="train_data.$kind.csv"
+ python reassign_mass_spec_training_data.py \
+ "$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2" \
+ --set-measurement-value 500 \
+ --out-csv "$TRAINING_DATA"
+ HYPERPARAMETERS=hyperparameters.production.yaml
+ fi
+
if [ "$kind" == "ms_only_0nm" ]
then
TRAINING_DATA="train_data.$kind.csv"
--
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