jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified January 22, 2020
jpayne@69: 
jpayne@69: Description:  Splits a file of various rRNAs into one file per type
jpayne@69: (16S, 18S, 5S, 23s).
jpayne@69: 
jpayne@69: Usage:  splitribo.sh in=<file,file> out=<pattern>
jpayne@69: 
jpayne@69: Standard parameters:
jpayne@69: in=<file>       Input file.
jpayne@69: out=<pattern>   Output file pattern, such as out_#.fa.  The # symbol is
jpayne@69:                 required and will be substituted by the type name, such as
jpayne@69:                 16S, to make out_16S.fa, for example.
jpayne@69: overwrite=f     (ow) Set to false to force the program to abort rather than
jpayne@69:                 overwrite an existing file.
jpayne@69: ziplevel=9      (zl) Set to 1 (lowest) through 9 (max) to change compression
jpayne@69:                 level; lower compression is faster.
jpayne@69: 
jpayne@69: types=16S,18S,5S,23S,m16S,m18S,p16S
jpayne@69:                 Align to these sequences.  Fewer types is faster.  m16S
jpayne@69:                 and m18S are mitochondrial; p16S is plastid (chloroplast).
jpayne@69: 
jpayne@69: Processing parameters:
jpayne@69: minid=0.59      Ignore alignments with identity lower than this to a 
jpayne@69:                 consensus sequences.
jpayne@69: refineid=0.70   Refine score by aligning to clade-specific consensus if
jpayne@69:                 the best alignment to a universal consensus is below this.
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 [[ $set == 1 ]]; then
jpayne@69: 		return
jpayne@69: 	fi
jpayne@69: 	freeRam 4000m 42
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: mergeribo() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP prok.SplitRibo $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: mergeribo "$@"