bracken

#!/bin/bash

#####################################################################
#bracken.sh checks that the Bracken files are present and generates the abundance estimation
#Copyright (C) 2016-2023 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
INPUT=""
OUTPUT=""
OUTREPORT=""
DATABASE=""
READ_LEN=100
THRESHOLD=10
LEVEL="S"

VERSION="2.9"
while getopts "t:i:o:r:d:w:l:v" OPTION
    do 
        case $OPTION in
            t)
                THRESHOLD=$OPTARG
                ;;
            r)
                READ_LEN=$OPTARG
                ;;
            l)
                LEVEL=$OPTARG
                ;;
            d)
                DATABASE=$OPTARG
                ;;
            i)
                INPUT=$OPTARG
                ;;
            o)
                OUTPUT=$OPTARG
                ;;
            w) 
                OUTREPORT=$OPTARG
                ;;
            v) 
                echo Bracken v${VERSION}
                exit 0
                ;;
            \?)
                echo "Usage: bracken -v -d MY_DB -i INPUT -o OUTPUT -w OUTREPORT -r READ_LEN -l LEVEL -t THRESHOLD"
                echo "  -v             Echoes the current software version and exits" 
                echo "  MY_DB          location of Kraken database" 
                echo "  INPUT          Kraken REPORT file to use for abundance estimation"
                echo "  OUTPUT         file name for Bracken default output" 
                echo "  OUTREPORT      New Kraken REPORT output file with Bracken read estimates"
                echo "  READ_LEN       read length to get all classifications for (default: 100)"
                echo "  LEVEL          level to estimate abundance at [options: D,P,C,O,F,G,S,S1,etc] (default: S)"
                echo "  THRESHOLD      number of reads required PRIOR to abundance estimation to perform reestimation (default: 0)"
                echo
                exit
                ;;
        esac
    done

if [[ "$DATABASE" =~ "/"$ ]]
then
    DATABASE=${DATABASE:0:-1}
fi
#Check if Kraken database exists
echo " >> Checking for Valid Options..."
if [ -d $DATABASE ] 
then 
    #Directory exists, check for databaseXmers.kmer_distrib
    if [ ! -f $DATABASE/database${READ_LEN}mers.kmer_distrib ] 
    then
        echo " ERROR: ${DATABASE}/database${READ_LEN}mers.kmer_distrib does not exist"
        echo "        Run bracken-build to generate the kmer distribution file." 
        exit
    fi
else 
    echo " ERROR: Kraken database ${DATABASE} does not exist"
    exit 
fi
#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
DIR=`dirname $(realpath $0 || echo $0)`
#cd $DIR
echo " >> Running Bracken " 
#Check to make sure input file exists 
if [ -f ${INPUT} ]
then 
    if [[ "${OUTREPORT}" = "" ]]
    then
        echo "      >> python src/est_abundance.py -i ${INPUT} -o ${OUTPUT} -k $DATABASE/database${READ_LEN}mers.kmer_distrib -l ${LEVEL} -t ${THRESHOLD}"
        python $DIR/src/est_abundance.py -i ${INPUT} \
            -o ${OUTPUT} \
            -k $DATABASE/database${READ_LEN}mers.kmer_distrib \
            -l ${LEVEL} \
            -t ${THRESHOLD}
    else
        echo "      >> python src/est_abundance.py -i ${INPUT} -o ${OUTPUT} -k $DATABASE/database${READ_LEN}mers.kmer_distrib -l ${LEVEL} -t ${THRESHOLD}"
        python $DIR/src/est_abundance.py -i ${INPUT} \
            -o ${OUTPUT} \
            --out-report ${OUTREPORT} \
            -k $DATABASE/database${READ_LEN}mers.kmer_distrib \
            -l ${LEVEL} \
            -t ${THRESHOLD}
    fi
else
    echo "  ERROR: Input file ${INPUT} does not exist" 
    echo "         If running kraken v1.0, run kraken-report"
    echo "         If running kraken v2.0, run kraken2 with the --report flag" 
    exit
fi
echo "  Bracken complete."