update

downloads-generation/models_class1_pan_refined/GENERATE.sh

@@ -58,32 +58,34 @@ MONOALLELIC_TRAIN="$(mhcflurry-downloads path models_class1_pan)/models.with_mas
 
 # ********************************************************
 # First we refine a single model excluding chromosome 1.
-echo "Beginning testing run."
-time python make_multiallelic_training_data.py \
-    --hits "$(mhcflurry-downloads path data_mass_spec_annotated)/annotated_ms.csv.bz2" \
-    --expression "$(mhcflurry-downloads path data_curated)/rna_expression.csv.bz2" \
-    --exclude-contig "1" \
-    --decoys-per-hit 1 \
-    --out train.multiallelic.no_chr1.csv
-
-time mhcflurry-multiallelic-refinement \
-    --monoallelic-data "$MONOALLELIC_TRAIN" \
-    --multiallelic-data train.multiallelic.no_chr1.csv \
-    --models-dir "$(mhcflurry-downloads path models_class1_pan)/models.with_mass_spec" \
-    --hyperparameters hyperparameters.yaml \
-    --out-affinity-predictor-dir $(pwd)/test_models.no_chr1.affinity \
-    --out-presentation-predictor-dir $(pwd)/test_models.no_chr1.presentation \
-    --worker-log-dir "$SCRATCH_DIR/$DOWNLOAD_NAME" \
-    $PARALLELISM_ARGS
-
-time mhcflurry-calibrate-percentile-ranks \
-    --models-dir $(pwd)/test_models.no_chr1.affinity   \
-    --match-amino-acid-distribution-data "$MONOALLELIC_TRAIN" \
-    --motif-summary \
-    --num-peptides-per-length 100000 \
-    --allele "HLA-A*02:01" "HLA-A*02:20" "HLA-C*02:10" \
-    --verbosity 1 \
-    $PARALLELISM_ARGS
+if false; then
+    echo "Beginning testing run."
+    time python make_multiallelic_training_data.py \
+        --hits "$(mhcflurry-downloads path data_mass_spec_annotated)/annotated_ms.csv.bz2" \
+        --expression "$(mhcflurry-downloads path data_curated)/rna_expression.csv.bz2" \
+        --exclude-contig "1" \
+        --decoys-per-hit 1 \
+        --out train.multiallelic.no_chr1.csv
+
+    time mhcflurry-multiallelic-refinement \
+        --monoallelic-data "$MONOALLELIC_TRAIN" \
+        --multiallelic-data train.multiallelic.no_chr1.csv \
+        --models-dir "$(mhcflurry-downloads path models_class1_pan)/models.with_mass_spec" \
+        --hyperparameters hyperparameters.yaml \
+        --out-affinity-predictor-dir $(pwd)/test_models.no_chr1.affinity \
+        --out-presentation-predictor-dir $(pwd)/test_models.no_chr1.presentation \
+        --worker-log-dir "$SCRATCH_DIR/$DOWNLOAD_NAME" \
+        $PARALLELISM_ARGS
+
+    time mhcflurry-calibrate-percentile-ranks \
+        --models-dir $(pwd)/test_models.no_chr1.affinity   \
+        --match-amino-acid-distribution-data "$MONOALLELIC_TRAIN" \
+        --motif-summary \
+        --num-peptides-per-length 100000 \
+        --allele "HLA-A*02:01" "HLA-A*02:20" "HLA-C*02:10" \
+        --verbosity 1 \
+        $PARALLELISM_ARGS
+fi
 
 # ********************************************************
 echo "Beginning production run"