File: preprocessing.sh

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#!/bin/sh

############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################


if [ -z "$1" ]
then
	echo Usage: $0 database.fasta
	echo Example: $0 SSURef_108_NR_tax_silva_v2.fasta
	exit
fi


tempfile=`basename $1`.tmp
indxfile=`basename $1`

echo Building taxonomy index for $1 ...
echo Temporary file: $tempfile
echo Index prefix: $indxfile

python3 preprocessing.py < $1 > $tempfile

bowtie-build $tempfile $indxfile

rm $tempfile