jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified December 22, 2021
jpayne@69: This script requires at least 52GB RAM.
jpayne@69: It is designed for NERSC and uses hard-coded paths.
jpayne@69: 
jpayne@69: Description:  Removes all reads that map to the cat, dog, mouse, or human genome with at least 95% identity after quality trimming.
jpayne@69: Removes approximately 98.6% of human 2x150bp reads, with zero false-positives to non-animals.
jpayne@69: NOTE!  This program uses hard-coded paths and will only run on Nersc systems.
jpayne@69: 
jpayne@69: Usage:  removecatdogmousehuman.sh in=<input file> outu=<clean output file>
jpayne@69: 
jpayne@69: Input may be fasta or fastq, compressed or uncompressed.
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: threads=auto        (t) Set number of threads to use; default is number of logical processors.
jpayne@69: overwrite=t         (ow) Set to false to force the program to abort rather than overwrite an existing file.
jpayne@69: interleaved=auto    (int) If true, forces fastq input to be paired and interleaved.
jpayne@69: trim=t              Trim read ends to remove bases with quality below minq.
jpayne@69:                     Values: t (trim both ends), f (neither end), r (right end only), l (left end only).
jpayne@69: untrim=t            Undo the trimming after mapping.
jpayne@69: minq=4              Trim quality threshold.
jpayne@69: ziplevel=2          (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
jpayne@69: outm=<file>         File to output the reads that mapped to human.
jpayne@69: 
jpayne@69: ***** All BBMap parameters can be used; run bbmap.sh for more details. *****
jpayne@69: 
jpayne@69: Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
jpayne@69: "
jpayne@69: }
jpayne@69: 
jpayne@69: #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69: pushd . > /dev/null
jpayne@69: DIR="${BASH_SOURCE[0]}"
jpayne@69: while [ -h "$DIR" ]; do
jpayne@69:   cd "$(dirname "$DIR")"
jpayne@69:   DIR="$(readlink "$(basename "$DIR")")"
jpayne@69: done
jpayne@69: cd "$(dirname "$DIR")"
jpayne@69: DIR="$(pwd)/"
jpayne@69: popd > /dev/null
jpayne@69: 
jpayne@69: #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69: CP="$DIR""current/"
jpayne@69: JNI="-Djava.library.path=""$DIR""jni/"
jpayne@69: JNI=""
jpayne@69: 
jpayne@69: z="-Xmx50g"
jpayne@69: z2="-Xms50g"
jpayne@69: set=0
jpayne@69: 
jpayne@69: if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
jpayne@69: 	usage
jpayne@69: 	exit
jpayne@69: fi
jpayne@69: 
jpayne@69: calcXmx () {
jpayne@69: 	source "$DIR""/calcmem.sh"
jpayne@69: 	setEnvironment
jpayne@69: 	parseXmx "$@"
jpayne@69: 	if [[ $set == 1 ]]; then
jpayne@69: 		return
jpayne@69: 	fi
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: function removecatdogmousehuman() {
jpayne@69: 	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBMap minratio=0.9 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 path=/global/cfs/cdirs/bbtools/mousecatdoghuman/ pigz unpigz zl=6 qtrim=r trimq=10 untrim idtag usemodulo printunmappedcount ztd=2 kfilter=25 maxsites=1 k=14 bloomfilter $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: removecatdogmousehuman "$@"