From 0c142dba39f2274371bd8ca745fd8390735dd469 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Wed, 1 Jan 2020 18:25:12 -0500
Subject: [PATCH] Add affinity_only model variant
---
.../models_class1_pan_variants/GENERATE.sh | 17 +++++++++++++++--
.../generate_hyperparameters.production.py | 2 +-
2 files changed, 16 insertions(+), 3 deletions(-)
diff --git a/downloads-generation/models_class1_pan_variants/GENERATE.sh b/downloads-generation/models_class1_pan_variants/GENERATE.sh
index bbbdb94b..3302dab7 100755
--- a/downloads-generation/models_class1_pan_variants/GENERATE.sh
+++ b/downloads-generation/models_class1_pan_variants/GENERATE.sh
@@ -68,7 +68,7 @@ then
python generate_hyperparameters.py hyperparameters.production.yaml compact_peptide > hyperparameters.compact_peptide.yaml
fi
-for kind in 34mer_sequence single_hidden_no_pretrain no_pretrain compact_peptide no_additional_ms ms_only
+for kind in 34mer_sequence single_hidden_no_pretrain no_pretrain compact_peptide no_additional_ms ms_only affinity_only
do
CONTINUE_INCOMPLETE_ARGS=""
if [ "$2" == "continue-incomplete" ] && [ -d "models.unselected.${kind}" ]
@@ -94,6 +94,10 @@ do
then
TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.mass_spec.csv.bz2"
fi
+ if [ "$kind" == "affinity_only" ]
+ then
+ TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.affinity.csv.bz2"
+ fi
mhcflurry-class1-train-pan-allele-models \
--data "$TRAINING_DATA" \
@@ -109,7 +113,7 @@ done
echo "Done training. Beginning model selection."
-for kind in single_hidden_no_pretrain no_pretrain 34mer_sequence compact_peptide no_additional_ms ms_only
+for kind in single_hidden_no_pretrain no_pretrain 34mer_sequence compact_peptide no_additional_ms ms_only affinity_only
do
MODELS_DIR="models.unselected.${kind}"
mhcflurry-class1-select-pan-allele-models \
@@ -141,3 +145,12 @@ done
split -b 2000M "$RESULT" "$PARTS"
echo "Split into parts:"
ls -lh "${PARTS}"*
+
+# Write out just the selected models
+# Move unselected into a hidden dir so it is excluded in the glob (*).
+mkdir .ignored
+mv models.unselected.* .ignored/
+RESULT="$SCRATCH_DIR/${DOWNLOAD_NAME}.selected.$(date +%Y%m%d).tar.bz2"
+tar -cjf "$RESULT" *
+mv .ignored/* . && rmdir .ignored
+echo "Created archive: $RESULT"
\ No newline at end of file
diff --git a/downloads-generation/models_class1_pan_variants/generate_hyperparameters.production.py b/downloads-generation/models_class1_pan_variants/generate_hyperparameters.production.py
index 0b7b520f..6dbf99bd 120000
--- a/downloads-generation/models_class1_pan_variants/generate_hyperparameters.production.py
+++ b/downloads-generation/models_class1_pan_variants/generate_hyperparameters.production.py
@@ -1 +1 @@
-../models_class1_pan_unselected/generate_hyperparameters.py
\ No newline at end of file
+../models_class1_pan/generate_hyperparameters.py
\ No newline at end of file
--
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