bracken-build

#!/bin/bash

#####################################################################
#bracken_build.sh creates the kmer distribution file for a single Kraken database
#Copyright (C) 2016-2022 Jennifer Lu, jlu26@jhmi.edu
#
#This file is part of Bracken.
#
#Bracken 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.
#
#This program 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 this program; if not, see <http://www.gnu.org/licenses/>.
#
#####################################################################

set -eu
THREADS=1
KMER_LEN=35
READ_LEN=100
DATABASE=""
KRAKEN="kraken"
KINSTALL=""
KTYPE=kraken2

VERSION="2.8"
while getopts "k:l:d:x:t:y:v" OPTION
    do
        case $OPTION in
            t)
                THREADS=$OPTARG
                ;;
            k)
                KMER_LEN=$OPTARG
                ;;
            l)
                READ_LEN=$OPTARG
                ;;
            d)
                DATABASE=$OPTARG
                ;;
            x)
                KINSTALL=$OPTARG
                ;;
            y) 
                KTYPE=$OPTARG
                ;;
            v) 
                echo bracken-build.sh v${VERSION}
                exit 0
                ;;
            \?)
                echo "Usage: bracken_build -v -k KMER_LEN -l READ_LEN -d MY_DB -x K_INSTALLATION -y K_TYPE -t THREADS"
                echo "  -v             Echoes the current software version and exits" 
                echo "  KMER_LEN       kmer length used to build the kraken database (default: 35)"
                echo "  THREADS        the number of threads to use when running kraken classification and the bracken scripts"
                echo "  READ_LEN       read length to get all classifications for (default: 100)"
                echo "  MY_DB          location of Kraken database"
                echo "  K_INSTALLATION location of the installed kraken/kraken-build scripts (default assumes scripts can be run from the user path)"
                echo "  K_TYPE         version of kraken to use (default = kraken2 - other options: kraken, krakenuniq)"
                exit
                ;;
        esac
    done
#Output command line options selected
echo " >> Selected Options:"
echo "       kmer length = $KMER_LEN"
echo "       read length = $READ_LEN"
echo "       database    = $DATABASE"
echo "       threads     = $THREADS"
echo "       kraken type = $KTYPE"
if [[ "$DATABASE" =~ "/"$ ]]
then
    DATABASE=${DATABASE:0:-1}
fi
#Check for Kraken version
if [ "$KINSTALL" == "" ]; then
    if [ "$KTYPE" == "kraken2" ]; then
        if hash kraken2 &> /dev/null; then
            KRAKEN="kraken2"
        else
            echo "Kraken 2 not installed. Please specify installation directory using -x flag"
            exit
        fi
    elif [ "$KTYPE" == "kraken" ]; then
        if hash kraken &> /dev/null; then
            KRAKEN="kraken"
        else
            echo "Kraken not installed. Please specify installation directory using -x flag"
            exit
        fi
    elif [ "$KTYPE" == "krakenuniq" ]; then
        if hash krakenuniq &> /dev/null; then
            KRAKEN="krakenuniq"
        else
            echo "Krakenuniq not installed. Please specify installation directory using -x flag"
            exit
        fi
    else
        echo "User must first specify/install kraken, krakenuniq, or kraken2 and/or specify installation directory of kraken/krakenuniq/kraken2 using -x flag"
        exit
    fi
else
    #user specified location of kraken installation 
    if [[ "$KINSTALL" =~ [^/]$ ]]
    then
        KINSTALL="$KINSTALL/"
    fi
    if [ -f ${KINSTALL}kraken2 ] && [ ${KTYPE} == "kraken2" ]; then
        KRAKEN="kraken2"
    elif [ -f ${KINSTALL}kraken ] && [ ${KTYPE} == "kraken" ]; then
        KRAKEN="kraken"
    elif [ -f ${KINSTALL}krakenuniq ] && [ ${KTYPE} == "krakenuniq" ]; then
        KRAKEN="krakenuniq"
    else
        echo "User must first specify/install kraken, krakenuniq, or kraken2 and/or specify installation directory of kraken/krakenuniq/kraken2 using -x flag"
        exit
    fi
fi
#Check if Kraken database exists
echo " >> Checking for Valid Options..."
if [ -d $DATABASE ]
then
    #Directory exists, check for taxonomy/nodes.dmp, library/ and for hash.k2d file
    if [ ! -d $DATABASE/library ]
    then
        echo " ERROR: Database library $DATABASE/library does not exist"
        exit
    elif [ ! -d $DATABASE/taxonomy ]
    then
        echo " ERROR : Database taxonomy $DATABASE/taxonomy does not exist"
        exit
    elif [ ! -f $DATABASE/taxonomy/nodes.dmp ]
    then
        echo " ERROR: Database taxonomy $DATABASE/taxonomy/nodes.dmp does not exist"
        exit
    elif [ $KRAKEN == "kraken2" ] && [ ! -f $DATABASE/hash.k2d ]
    then
        echo " ERROR: Kraken2 Database incomplete: $DATABASE/hash.k2d does not exist"
        exit
    elif [ $KRAKEN == "kraken" ] && [ ! -f $DATABASE/database.kdb ]
    then
        echo " ERROR: Kraken Database incomplete: $DATABASE/database.kdb does not exist"
        exit
    elif [ $KRAKEN == "krakenuniq" ] && [ ! -f $DATABASE/database.kdb ]
    then
        echo " ERROR: KrakenUniq Database incomplete: $DATABASE/database.kdb does not exist"
        exit
    fi
else
    echo " ERROR: Kraken database $DATABASE" does not exist
    exit
fi
#See if database.kraken exists, if not, create
echo " >> Creating database.kraken [if not found]"
if [ -s $DATABASE/database.kraken ]
then
    #database.kraken exists, skip
    echo "          database.kraken exists, skipping creation...."
elif [ -s $DATABASE/database.kraken.tsv ]
then
    #database.kraken.tsv exists, skip
    echo "          database.kraken.tsv exists, skipping creation...."
    ln -s $DATABASE/database.kraken.tsv $DATABASE/database.kraken
elif [ $KRAKEN == "kraken2" ]
then
    #database.kraken not found, must create
    echo "      >> ${KINSTALL}kraken2 --db $DATABASE --threads ${THREADS} <( find -L $DATABASE/library \( -name "*.fna" -o -name "*.fa" -o -name "*.fasta" \) -exec cat {} + ) > $DATABASE/database.kraken"

    ${KINSTALL}kraken2 --db $DATABASE --threads ${THREADS} <( find -L $DATABASE/library \( -name "*.fna" -o -name "*.fa" -o -name "*.fasta" \) -exec cat {} + ) > $DATABASE/database.kraken
elif [ $KRAKEN == "krakenuniq"]
then 
    #database.kraken not found, must create
    echo "      >> ${KINSTALL}krakenuniq --db $DATABASE --threads ${THREADS} <( find -L $DATABASE/library \( -name "*.fna" -o -name "*.fa" -o -name "*.fasta" \) -exec cat {} + ) > $DATABASE/database.kraken"
    ${KINSTALL}krakenuniq --db $DATABASE --threads ${THREADS} <( find -L $DATABASE/library \( -name "*.fna" -o -name "*.fa" -o -name "*.fasta" \) -exec cat {} + ) > $DATABASE/database.kraken
else
    #database.kraken not found, must create
    echo "      >> ${KINSTALL}kraken --db $DATABASE --threads ${THREADS} <( find -L $DATABASE/library \( -name "*.fna" -o -name "*.fa" -o -name "*.fasta" \) -exec cat {} + ) > $DATABASE/database.kraken"
    ${KINSTALL}kraken --db $DATABASE --threads ${THREADS} <( find -L $DATABASE/library \( -name "*.fna" -o -name "*.fa" -o -name "*.fasta" \) -exec cat {} + ) > $DATABASE/database.kraken
fi
echo "          Finished creating database.kraken [in DB folder]"
#Generate databaseXmers.kmer_distrib
#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
DIR=`dirname $(readlink $0 || echo $0)`
#cd $DIR
echo " >> Creating database${READ_LEN}mers.kmer_distrib "
if [ -f $DIR/src/kmer2read_distr ]; then
    $DIR/src/kmer2read_distr --seqid2taxid $DATABASE/seqid2taxid.map --taxonomy $DATABASE/taxonomy/ --kraken $DATABASE/database.kraken --output $DATABASE/database${READ_LEN}mers.kraken -k ${KMER_LEN} -l ${READ_LEN} -t ${THREADS}
    python $DIR/src/generate_kmer_distribution.py -i $DATABASE/database${READ_LEN}mers.kraken -o $DATABASE/database${READ_LEN}mers.kmer_distrib
# check if kmer2read_distr is in PATH
elif [ -f $(command -v kmer2read_distr) ]; then
    kmer2read_distr --seqid2taxid $DATABASE/seqid2taxid.map --taxonomy $DATABASE/taxonomy/ --kraken $DATABASE/database.kraken --output $DATABASE/database${READ_LEN}mers.kraken -k ${KMER_LEN} -l ${READ_LEN} -t ${THREADS}
    if [ -f $(command -v generate_kmer_distribution.py) ]; then
        python $(command -v generate_kmer_distribution.py) -i $DATABASE/database${READ_LEN}mers.kraken -o $DATABASE/database${READ_LEN}mers.kmer_distrib
    else
        echo "      ERROR: generate_kmer_distribution.py script not found. "
        echo "          Run 'sh install_bracken.sh' to generate the kmer2read_distr script."
        echo "          Alternatively, cd to BRACKEN_FOLDER/src/ and run 'make'"
        exit
    fi
else
    echo "      ERROR: kmer2read_distr program not found. "
    echo "          Run 'sh install_bracken.sh' to generate the kmer2read_distr script."
    echo "          Alternatively, cd to BRACKEN_FOLDER/src/ and run 'make'"
    exit
fi
echo "          Finished creating database${READ_LEN}mers.kraken and database${READ_LEN}mers.kmer_distrib [in DB folder]"
echo "          *NOTE: to create read distribution files for multiple read lengths, "
echo "                 rerun this script specifying the same database but a different read length"
echo
echo "Bracken build complete."