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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified July 30, 2024
Description: Selects a subset of files from an all-to-all identity
comparison. The subset will contain exactly X files with maximal
pairwise ANI, or all files with at most Y pairwise identity.
This program is similar to representative.sh but does not use taxonomy.
Input should be in 3+ column TSV format (first 3 are required):
(query, ref, ANI)
...as produced by CompareSketch when run like this:
comparesketch.sh ata format=3 includeself perfile records=99999 *.fasta
Usage: picksubset.sh in=<file> out=<file> invalid=<file> files=<number>
Parameters:
in= Input file comparing all-to-all comparisons.
out= Output file for the list of files to retain.
invalid= Output file for the list of files to discard.
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
files=0 Number of files to retain.
ani=0 Maximum pairwise ANI allowed, expressed as a percent.
NOTE: files or ani, or both, must be set.
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 around 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.
"
}
#This block allows symlinked shellscripts to correctly set classpath.
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="-Xmx2g"
z2="-Xms2g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
picksubset() {
local CMD="java $EA $EOOM $z -cp $CP jgi.PickSubset $@"
echo $CMD >&2
eval $CMD
}
picksubset "$@"
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