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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified January 22, 2020
Description: Splits a file of various rRNAs into one file per type
(16S, 18S, 5S, 23s).
Usage: splitribo.sh in=<file,file> out=<pattern>
Standard parameters:
in=<file> Input file.
out=<pattern> Output file pattern, such as out_#.fa. The # symbol is
required and will be substituted by the type name, such as
16S, to make out_16S.fa, for example.
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
ziplevel=9 (zl) Set to 1 (lowest) through 9 (max) to change compression
level; lower compression is faster.
types=16S,18S,5S,23S,m16S,m18S,p16S
Align to these sequences. Fewer types is faster. m16S
and m18S are mitochondrial; p16S is plastid (chloroplast).
Processing parameters:
minid=0.59 Ignore alignments with identity lower than this to a
consensus sequences.
refineid=0.70 Refine score by aligning to clade-specific consensus if
the best alignment to a universal consensus is below this.
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.
-eoom This flag will cause the process to exit if an out-of-memory
exception occurs. Requires Java 8u92+.
-da Disable assertions.
Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
"
}
pushd . > /dev/null
DIR="${BASH_SOURCE[0]}"
while [ -h "$DIR" ]; do
cd "$(dirname "$DIR")"
DIR="$(readlink "$(basename "$DIR")")"
done
cd "$(dirname "$DIR")"
DIR="$(pwd)/"
popd > /dev/null
#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
CP="$DIR""current/"
z="-Xmx4g"
z2="-Xms4g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 4000m 42
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
mergeribo() {
local CMD="java $EA $EOOM $z -cp $CP prok.SplitRibo $@"
echo $CMD >&2
eval $CMD
}
mergeribo "$@"
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