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#!/bin/bash
#
# Create allele sequences.
# Requires: clustalo, wget
#
set -e
set -x
DOWNLOAD_NAME=allele_sequences
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
which clustalo
clustalo --version
cd $SCRATCH_DIR/$DOWNLOAD_NAME
cp $SCRIPT_DIR/make_allele_sequences.py .
cp $SCRIPT_DIR/filter_sequences.py .
cp $SCRIPT_DIR/class1_pseudosequences.csv .
cp $SCRIPT_ABSOLUTE_PATH .
# Generate sequences
# Training data is used to decide which additional positions to include in the
# allele sequences to differentiate alleles that have identical traditional
# pseudosequences but have associated training data
TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.with_mass_spec.csv.bz2"
bzcat "$(mhcflurry-downloads path data_curated)/curated_training_data.with_mass_spec.csv.bz2" \
| cut -f 1 -d , | uniq | sort | uniq | grep -v allele > training_data.alleles.txt
wget -q ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/fasta/A_prot.fasta
wget -q ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/fasta/B_prot.fasta
wget -q ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/fasta/C_prot.fasta
wget -q ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/fasta/E_prot.fasta
wget -q ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/fasta/F_prot.fasta
wget -q ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/fasta/G_prot.fasta
wget -q ftp://ftp.ebi.ac.uk/pub/databases/ipd/mhc/MHC_prot.fasta
wget -q https://www.uniprot.org/uniprot/P01899.fasta # H-2
python filter_sequences.py *.fasta --out class1.fasta
time clustalo -i class1.fasta -o class1.aligned.fasta
time python make_allele_sequences.py \
class1.aligned.fasta \
--recapitulate-sequences class1_pseudosequences.csv \
--differentiate-alleles training_data.alleles.txt \
--out-csv allele_sequences.csv
# Cleanup
gzip -f class1.fasta
gzip -f class1.aligned.fasta
rm *.fasta
cp $SCRIPT_ABSOLUTE_PATH .
bzip2 LOG.txt
tar -cjf "../${DOWNLOAD_NAME}.tar.bz2" *
echo "Created archive: $SCRATCH_DIR/$DOWNLOAD_NAME.tar.bz2"