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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified September 4, 2019
Description: Makes a representative set of taxa from all-to-all identity
comparison. Input should be in 3+ column TSV format (first 3 are required):
(query, ref, ANI, qsize, rsize, qbases, rbases)
...as produced by CompareSketch with format=3 and usetaxidname.
Additional columns are allowed and will be ignored.
Usage: representative.sh in=<input file> out=<output file>
Parameters:
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
threshold=0 Ignore edges under threshold value. This also affects the
choice of centroids; a high threshold gives more weight to
higher-value edges.
minratio=0 Ignores edges with a ratio below this value.
invertratio=f Invert the ratio when greater than 1.
printheader=t Print a header line in the output.
printsize=t Print the size of retained nodes.
printclusters=t Print the nodes subsumed by each retained node.
minsize=0 Ignore nodes under this size (in unique kmers).
maxsize=0 If positive, ignore nodes over this size (unique kmers).
minbases=0 Ignore nodes under this size (in total bases).
maxbases=0 If positive, ignore nodes over this size (total bases).
Taxonomy parameters:
level= Taxonomic level, such as phylum. Filtering will operate on
sequences within the same taxonomic level as specified ids.
If not set, only matches to a node or its descendants will
be considered.
ids= Comma-delimited list of NCBI numeric IDs. Can also be a
file with one taxID per line.
names= Alternately, a list of names (such as 'Homo sapiens').
Note that spaces need special handling.
include=f 'f' will discard filtered sequences, 't' will keep them.
tree=<file> Specify a TaxTree file like tree.taxtree.gz.
On Genepool, use 'auto'.
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="-Xmx4g"
z2="-Xms4g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 4000m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
a_sample_mt() {
local CMD="java $EA $EOOM $z -cp $CP jgi.RepresentativeSet $@"
echo $CMD >&2
eval $CMD
}
a_sample_mt "$@"
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