addssu.sh

#!/bin/bash

usage(){
echo "
Written by Brian Bushnell
Last modified Jan 29, 2020

Description:  Adds, removes, or replaces SSU sequence of existing sketches.
Sketches and SSU fasta files must be annotated with TaxIDs.

Usage:           addssu.sh in=a.sketch out=b.sketch 16S=16S.fa 18S=18S.fa

Standard parameters:
in=<file>       Input sketch file.
out=<file>      Output sketch file.

Additional file parameters (optional):
16S=<file>      A fasta file of 16S sequences.  These should be renamed
                so that they start with tid|# where # is the taxID.
                Should not contain organelle rRNA.
18S=<file>      A fasta file of 18S sequences.  These should be renamed
                so that they start with tid|# where # is the taxID.
                Should not contain organelle rRNA.
tree=auto       Path to TaxTree, if performing prok/euk-specific operations.

Processing parameters:
preferSSUMap=f
preferSSUMapEuks=f
preferSSUMapProks=f
SSUMapOnly=f
SSUMapOnlyEuks=f
SSUMapOnlyProks=f
clear16S=f
clear18S=f
clear16SEuks=f
clear18SEuks=f
clear16SProks=f
clear18SProks=f


Java Parameters:
-Xmx            This will set Java's memory usage, overriding autodetection.
                -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
                    The max is typically 85% of physical memory.
-da             Disable assertions.

For more detailed information, please read /bbmap/docs/guides/BBSketchGuide.txt.
Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
For documentation and the latest version, visit: https://bbmap.org
"
}

if [ -z "$1" ] || [ "$1" = "-h" ] || [ "$1" = "--help" ]; then
	usage
	exit
fi

resolveSymlinks(){
	SCRIPT="$(cd "$(dirname "$0")" && pwd)/$(basename "$0")"
	while [ -h "$SCRIPT" ]; do
		DIR="$(dirname "$SCRIPT")"
		SCRIPT="$(readlink "$SCRIPT")"
		[ "${SCRIPT#/}" = "$SCRIPT" ] && SCRIPT="$DIR/$SCRIPT"
	done
	DIR="$(cd "$(dirname "$SCRIPT")" && pwd)"
	if [ -f "$DIR/bbtools.jar" ]; then
		CP="$DIR/bbtools.jar"
	else
		CP="$DIR/current/"
	fi
}

setEnv(){
	. "$DIR/javasetup.sh"
	. "$DIR/memdetect.sh"

	parseJavaArgs "--xmx=4g" "--xms=4g" "--mode=fixed" "$@"
	setEnvironment
}

launch() {
	CMD="java $EA $EOOM $SIMD $XMX $XMS -cp $CP sketch.AddSSU $@"
	echo "$CMD" >&2
	eval $CMD
}

resolveSymlinks
setEnv "$@"
launch "$@"