From 1920478f32d53705c818058955814aaeea0987a8 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Tue, 7 Jan 2020 16:58:33 -0500
Subject: [PATCH] more variants
---
.../models_class1_pan_variants/GENERATE.sh | 41 ++++++++++++++++++-
1 file changed, 39 insertions(+), 2 deletions(-)
diff --git a/downloads-generation/models_class1_pan_variants/GENERATE.sh b/downloads-generation/models_class1_pan_variants/GENERATE.sh
index 76737300..bbb61903 100755
--- a/downloads-generation/models_class1_pan_variants/GENERATE.sh
+++ b/downloads-generation/models_class1_pan_variants/GENERATE.sh
@@ -62,13 +62,18 @@ if [ "$2" != "continue-incomplete" ]
then
cp $SCRIPT_DIR/generate_hyperparameters.production.py .
cp $SCRIPT_DIR/generate_hyperparameters.py .
+ cp $SCRIPT_DIR/reassign_mass_spec_training_data.py .
python generate_hyperparameters.production.py > hyperparameters.production.yaml
python generate_hyperparameters.py hyperparameters.production.yaml no_pretrain > hyperparameters.no_pretrain.yaml
python generate_hyperparameters.py hyperparameters.no_pretrain.yaml single_hidden > hyperparameters.single_hidden_no_pretrain.yaml
python generate_hyperparameters.py hyperparameters.production.yaml compact_peptide > hyperparameters.compact_peptide.yaml
fi
-for kind in no_additional_ms ms_only no_pretrain compact_peptide 34mer_sequence single_hidden_no_pretrain affinity_only
+#VARIANTS=( no_additional_ms_0nm 0nm ms_only_0nm no_additional_ms ms_only no_pretrain compact_peptide 34mer_sequence single_hidden_no_pretrain affinity_only )
+VARIANTS=( no_additional_ms_0nm 0nm ms_only_0nm no_additional_ms ms_only no_pretrain compact_peptide 34mer_sequence )
+
+
+for kind in "${variants[@]}"
do
CONTINUE_INCOMPLETE_ARGS=""
if [ "$2" == "continue-incomplete" ] && [ -d "models.unselected.${kind}" ]
@@ -91,11 +96,43 @@ do
TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.no_additional_ms.csv.bz2"
HYPERPARAMETERS=hyperparameters.production.yaml
fi
+
+ if [ "$kind" == "no_additional_ms_0nm" ]
+ then
+ TRAINING_DATA="train_data.no_additional_ms_0nm.csv"
+ python reassign_mass_spec_training_data.py \
+ "$(mhcflurry-downloads path data_curated)/curated_training_data.no_additional_ms.csv.bz2" \
+ --set-measurement-value 0 \
+ --out-csv "$TRAINING_DATA"
+ HYPERPARAMETERS=hyperparameters.production.yaml
+ fi
+
+ if [ "$kind" == "0nm" ]
+ then
+ TRAINING_DATA="train_data.0nm.csv"
+ python reassign_mass_spec_training_data.py \
+ "$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2" \
+ --set-measurement-value 0 \
+ --out-csv "$TRAINING_DATA"
+ HYPERPARAMETERS=hyperparameters.production.yaml
+ fi
+
+ if [ "$kind" == "ms_only_0nm" ]
+ then
+ TRAINING_DATA="train_data.ms_only_0nm.csv"
+ python reassign_mass_spec_training_data.py \
+ "$(mhcflurry-downloads path data_curated)/curated_training_data.mass_spec.csv.bz2" \
+ --set-measurement-value 0 \
+ --out-csv "$TRAINING_DATA"
+ HYPERPARAMETERS=hyperparameters.production.yaml
+ fi
+
if [ "$kind" == "ms_only" ]
then
TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.mass_spec.csv.bz2"
HYPERPARAMETERS=hyperparameters.production.yaml
fi
+
if [ "$kind" == "affinity_only" ]
then
TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.affinity.csv.bz2"
@@ -116,7 +153,7 @@ done
echo "Done training. Beginning model selection."
-for kind in no_additional_ms ms_only no_pretrain compact_peptide 34mer_sequence single_hidden_no_pretrain affinity_only
+for kind in "${variants[@]}"
do
MODELS_DIR="models.unselected.${kind}"
mhcflurry-class1-select-pan-allele-models \
--
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