jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Shijie Yao 
jpayne@69: Last modified May 31, 2018
jpayne@69: 
jpayne@69: Description: DNA Tetramer analysis.
jpayne@69: DNA tetramers are counted for each sub-sequence of window size in the sequence.  
jpayne@69: The window slides along the sequence by the step length.
jpayne@69: Sub-sequence shorter than the window size is ignored. Tetramers containing N are ignored. 
jpayne@69: 
jpayne@69: Usage: TetramerFreq.sh in=<input file> out=<output file> step=500 window=2000
jpayne@69: 
jpayne@69: Input may be fasta or fastq, compressed or uncompressed.
jpayne@69: 
jpayne@69: Standard parameters:
jpayne@69: in=<file>       DNA sequence input file 
jpayne@69: out=<file>      Output file name
jpayne@69: step/s=INT      Step size (default 500) 
jpayne@69: window/w=INT    Window size (default 2kb); <=0 turns windowing off (e.g. short reads)
jpayne@69: short=T/F       Print lines for sequences shorter than window (default F)
jpayne@69: k=INT           Kmer length (default 4)
jpayne@69: 
jpayne@69: Java Parameters:
jpayne@69: -Xmx            This will set Java's memory usage, overriding autodetection.
jpayne@69:                 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
jpayne@69:                 specify 200 megs. The max is typically 85% of physical memory.
jpayne@69: -eoom           This flag will cause the process to exit if an out-of-memory
jpayne@69:                 exception occurs.  Requires Java 8u92+.
jpayne@69: -da             Disable assertions.
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="-Xmx4g"
jpayne@69: z2="-Xms4g"
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 [[ $set == 1 ]]; then
jpayne@69: 		return
jpayne@69: 	fi
jpayne@69: 	freeRam 4000m 84
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: tetramerfreq () {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP jgi.TetramerFrequencies $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: tetramerfreq "$@"