Download the latest Uniprot (Swissprot+Trembl) release, make a BLAST database

download-uniprot-release.sh

#!/bin/bash

set -e
# Downloads the lastet release of Uniprot, putting it in a release-specific directory.
# Creates associated BLAST databases.

# We need makeblastdb on our PATH, somehow
# module load blast

# Better to use a stable DOWNLOAD_TMP name to support resuming downloads
#DOWNLOAD_TMP=$(mktemp -d _downloading-XXXX)
DOWNLOAD_TMP=_downloading

mkdir -p ${DOWNLOAD_TMP}
cd ${DOWNLOAD_TMP}

wget -c "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/RELEASE.metalink"
# Extract the release name (like 2017_10 or 2017_1)
RELEASE=$(grep -oP '(?<=<version>)(\d\d\d\d\_\d?\d)(?=<\/version>)' RELEASE.metalink)

wget -c "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz"
wget -c "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz"
wget -c "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/reldate.txt"
wget -c "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/README"
wget -c "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/LICENSE"

cd ..
mkdir ${RELEASE}
mv ${DOWNLOAD_TMP}/* ${RELEASE}
rmdir ${DOWNLOAD_TMP}
cd ${RELEASE}

gunzip uniprot_sprot.fasta.gz
gunzip uniprot_trembl.fasta.gz

cat uniprot_sprot.fasta uniprot_trembl.fasta >uniprot_${RELEASE}.fasta
makeblastdb -in uniprot_${RELEASE}.fasta -out uniprot_${RELEASE} -dbtype prot -parse_seqids -title uniprot_${RELEASE}
makeblastdb -in uniprot_sprot.fasta -out uniprot_sprot -dbtype prot -parse_seqids -title uniprot_sprot
makeblastdb -in uniprot_trembl.fasta -out uniprot_trembl -dbtype prot -parse_seqids -title uniprot_trembl

cd ..