Add models_class1_with_mass_spec downloads

downloads-generation/models_class1_with_mass_spec/GENERATE.sh

+#!/bin/bash
+#
+# Model select MHCflurry Class I models that were trained on mass-spec. Model
+# selection uses both mass-spec and affinity data.
+#
+set -e
+set -x
+
+DOWNLOAD_NAME=models_class1_with_mass_spec
+SCRATCH_DIR=${TMPDIR-/tmp}/mhcflurry-downloads-generation
+SCRIPT_ABSOLUTE_PATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/$(basename "${BASH_SOURCE[0]}")"
+SCRIPT_DIR=$(dirname "$SCRIPT_ABSOLUTE_PATH")
+
+mkdir -p "$SCRATCH_DIR"
+rm -rf "$SCRATCH_DIR/$DOWNLOAD_NAME"
+mkdir "$SCRATCH_DIR/$DOWNLOAD_NAME"
+
+# Send stdout and stderr to a logfile included with the archive.
+exec >  >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt")
+exec 2> >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt" >&2)
+
+# Log some environment info
+date
+pip freeze
+git status
+
+cd $SCRATCH_DIR/$DOWNLOAD_NAME
+cp $SCRIPT_DIR/write_validation_data.py .
+
+mkdir models
+
+GPUS=$(nvidia-smi -L 2> /dev/null | wc -l) || GPUS=0
+echo "Detected GPUS: $GPUS"
+
+PROCESSORS=$(getconf _NPROCESSORS_ONLN)
+echo "Detected processors: $PROCESSORS"
+
+python ./write_validation_data.py \
+    --include "$(mhcflurry-downloads path data_curated)/curated_training_data.with_mass_spec.csv.bz2" \
+    --exclude "$(mhcflurry-downloads path models_class1_unselected_with_mass_spec)/models/train_data.csv.bz2" \
+    --only-alleles-present-in-exclude \
+    --out-data test.csv \
+    --out-summary test.summary.csv
+
+wc -l test.csv
+
+time mhcflurry-class1-select-allele-specific-models \
+    --data test.csv \
+    --models-dir "$(mhcflurry-downloads path models_class1_unselected)/models" \
+    --out-models-dir models \
+    --scoring combined:mass-spec,mse,consensus \
+    --consensus-num-peptides-per-length 10000 \
+    --combined-min-models 8 \
+    --combined-max-models 16 \
+    --unselected-accuracy-scorer combined:mass-spec,mse \
+    --unselected-accuracy-percentile-threshold 95 \
+    --mass-spec-min-measurements 500 \
+    --num-jobs $(expr $PROCESSORS \* 2) --gpus $GPUS --max-workers-per-gpu 2 --max-tasks-per-worker 1
+
+time mhcflurry-calibrate-percentile-ranks \
+    --models-dir models \
+    --num-peptides-per-length 100000 \
+    --num-jobs $(expr $PROCESSORS \* 2) --gpus $GPUS --max-workers-per-gpu 2 --max-tasks-per-worker 50
+
+cp $SCRIPT_ABSOLUTE_PATH .
+bzip2 LOG.txt
+tar -cjf "../${DOWNLOAD_NAME}.tar.bz2" *
+
+echo "Created archive: $SCRATCH_DIR/$DOWNLOAD_NAME.tar.bz2"