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metacache-build-refseq
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metacache-build-refseq
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#!/bin/bash
# Copyright 2016-2021, André Müller <[email protected]>
#
# This file is part of the MetaCache taxonomic sequence classification tool.
#
# MetaCache is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MetaCache is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with MetaCache. If not, see <http://www.gnu.org/licenses/>.
# This script will download complete bacterial and virus genomes from
# the NCBI RefSeq project and build a classification database.
set -u # Protect against uninitialized vars.
set -e # Stop on error
MODE=standard
if [ $# -lt 1 ]; then
echo "Building database for NCBI RefSeq complete bacterial and virus genomes."
echo "Usage: $0 (big|standard|small)"
fi
# download-ncbi-genomes <sublibrary> <target folder>
./download-ncbi-genomes refseq/bacteria genomes
./download-ncbi-genomes refseq/viral genomes
./download-ncbi-genomes refseq/archaea genomes
# download-ncbi-taxonomy <target folder>
./download-ncbi-taxonomy genomes/taxonomy
# ./download-ncbi-taxmaps genomes/taxonomy
case "$MODE" in
"big")
./metacache build refseq_big genomes/refseq -taxonomy genomes/taxonomy -kmerlen 16 -winlen 127 -sketchlen 32
;;
"standard")
./metacache build refseq genomes/refseq -taxonomy genomes/taxonomy -kmerlen 16 -winlen 127 -sketchlen 16
;;
"small")
./metacache build refseq_small genomes/refseq -taxonomy genomes/taxonomy -kmerlen 16 -winlen 255 -sketchlen 16
;;
esac