jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified October 17, 2019
jpayne@69: 
jpayne@69: Description:  Generates a random, (probably) repeat-free genome.
jpayne@69: 
jpayne@69: Usage:  randomgenome.sh len=<total size> chroms=<int> gc=<float> out=<file>
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: out=<file>      Output.
jpayne@69: overwrite=f     (ow) Set to false to force the program to abort rather than
jpayne@69:                 overwrite an existing file.
jpayne@69: len=100000      Total genome size.
jpayne@69: chroms=1        Number of pieces.
jpayne@69: gc=0.5          GC fraction.
jpayne@69: nopoly=f        Ban homopolymers.
jpayne@69: pad=0           Add this many Ns to contig ends; does not count toward 
jpayne@69:                 genome size.
jpayne@69: seed=-1         Set to a positive number for deterministic output.
jpayne@69: amino=f         Produce random amino acids instead of nucleotides.
jpayne@69: includestop=f   Include stop codons in random amino sequences.
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: 
jpayne@69: z="-Xmx200m"
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 "$@"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: randomgenome() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP jgi.RandomGenome $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: randomgenome "$@"