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#!/bin/bash
#
set -x
DOWNLOAD_NAME=models_class1_kim_benchmark
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")
export PYTHONUNBUFFERED=1
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/curate.py .
cp $SCRIPT_DIR/write_validation_data.py .
time python curate.py \
--data-kim2014 \
"$(mhcflurry-downloads path data_published)/bdata.2009.mhci.public.1.txt" \
--out-csv train.csv
bzip2 train.csv
mkdir models
cp $SCRIPT_DIR/class1_pseudosequences.csv .
python $SCRIPT_DIR/generate_hyperparameters.py > hyperparameters.yaml
GPUS=$(nvidia-smi -L 2> /dev/null | wc -l) || GPUS=0
echo "Detected GPUS: $GPUS"
PROCESSORS=$(getconf _NPROCESSORS_ONLN)
echo "Detected processors: $PROCESSORS"
time mhcflurry-class1-train-allele-specific-models \
--data "train.csv.bz2" \
--allele-sequences class1_pseudosequences.csv \
--hyperparameters hyperparameters.yaml \
--out-models-dir models \
--held-out-fraction-reciprocal 10 \
--min-measurements-per-allele 20 \
--num-jobs $(expr $PROCESSORS \* 2) --gpus $GPUS --max-workers-per-gpu 2 --max-tasks-per-worker 50
time python ./write_validation_data.py \
--include "train.csv.bz2" \
--exclude "models/train_data.csv.bz2" \
--only-alleles-present-in-exclude \
--out-data test.csv \
--out-summary test.summary.csv
wc -l test.csv
mkdir selected-models
time mhcflurry-class1-select-allele-specific-models \
--data test.csv \
--models-dir models \
--out-models-dir selected-models \
--scoring combined:mse,consensus \
--consensus-num-peptides-per-length 10000 \
--combined-min-models 8 \
--combined-max-models 16 \
--num-jobs $(expr $PROCESSORS \* 2) --gpus $GPUS --max-workers-per-gpu 2 --max-tasks-per-worker 5
time mhcflurry-calibrate-percentile-ranks \
--models-dir selected-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"