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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified Oct 30, 2023
Description: Scores sequences using a neural network. This is similar
to scoresequence.sh but multithreaded and with more filtering options.
Usage: netfilter.sh in=<sequences> out=<pass> outu=<fail> net=<net file>
Input may be fasta or fastq, compressed or uncompressed.
Standard parameters:
in=<file> Input sequences.
out=<file> Sequences passing the filter.
outu=<file> Sequences failing the filter.
net=<file> Network file to apply to the sequences.
hist=<file> Histogram of scores (x100, so 0-1 maps to 0-100).
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
Processing parameters:
rcomp=f Use the max score of a sequence and its reverse complement.
parse=f Parse sequence headers for 'result=' to determine whether
they are positive or negative examples. Positive examples
should be annotated with result=1, and negative with result=0.
annotate=f Rename output sequences by appending 'score='.
filter=t Retain only reads above or below a cutoff. Setting the cutoff
or highpass flag will automatically set this to true.
cutoff=auto Score cutoff for filtering; scores mostly range from 0 to 1.
'auto' will use the cutoff embedded in the network.
highpass=t Retain sequences ABOVE cutoff if true, else BELOW cutoff.
scoremode= single (default): Apply the network once to each sequence.
If the sequence is longer than the network's inputs, use the
first X bases.
average: Apply the network to the sequence once every
'stepsize' bases, and use the average. May be slow.
max: Like average, but uses the maximum score.
min: Like average, but uses the minimum score.
pairmode= average (default): For paired reads, average the two scores.
max: Use the higher of the two scores.
min: Use the lower of the two scores.
stepsize=1 If scoremode is other than 'single', score a window every
this many bases. The window width is defined by the network.
Higher values of stepsize are faster.
overlap= This can be set instead of stepsize; if either flag is used it
will override the other. Setting overlap will make windows
overlap that much, so 'overlap=0' is equivalent to 'stepsize=W'
where W is the width of the network in bases.
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.
"
}
#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 "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 2000m 20
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
score() {
local CMD="java $EA $EOOM $z $z2 $SIMD -cp $CP ml.NetFilter $@"
echo $CMD >&2
eval $CMD
}
score "$@"
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