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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified October 6, 2022
Description: Sorts reads by name or other keys such as length,
quality, mapping position, flowcell coordinates, or taxonomy.
Writes temp files if memory is exceeded.
Usage: sortbyname.sh in=<file> out=<file>
Input may be fasta, fastq, or sam, compressed or uncompressed.
Temp files will use the same format as the output. Pairs are
kept together if reads are paired, and in2/out2 may be used for that.
Example 1 - sort by name:
sortbyname.sh in=raw.fq out=sorted.fq
Example 2 - sort by sequence:
sortbyname.sh in=raw.fq out=sorted.fq sequence
Example 3 - sort by mapping position:
sortbyname.sh in=mapped.sam out=sorted.sam position
Parameters:
in=<file> Input file.
out=<file> Output file.
name=t Sort reads by name.
length=f Sort reads by length.
quality=f Sort reads by quality.
position=f Sort reads by position (for mapped reads).
taxa=f Sort reads by taxonomy (for NCBI naming convention).
sequence=f Sort reads by sequence, alphabetically.
clump=f Sort reads by shared kmers, like Clumpify.
flowcell=f Sort reads by flowcell coordinates.
shuffle=f Shuffle reads randomly (untested).
list=<file> Sort reads according to this list of names.
ascending=t Sort ascending.
Memory parameters (you might reduce these if you experience a crash)
memmult=0.30 Write a temp file when used memory exceeds this fraction
of available memory.
memlimit=0.65 Wait for temp files to finish writing until used memory
drops below this fraction of available memory.
delete=t Delete temporary files.
allowtemp=t Allow writing temporary files.
Taxonomy-sorting parameters (for taxa mode only):
tree= Specify a taxtree file. On Genepool, use 'auto'.
gi= Specify a gitable file. On Genepool, use 'auto'.
accession= Specify one or more comma-delimited NCBI accession to
taxid files. On Genepool, use 'auto'.
Note: name, length, and quality are mutually exclusive.
Sorting by quality actually sorts by average expected error rate,
so ascending will place the highest-quality reads first.
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 [[ $set == 1 ]]; then
return
fi
freeRam 2000m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
sortbyname() {
local CMD="java $EA $EOOM $z $z2 -cp $CP sort.SortByName $@"
echo $CMD >&2
eval $CMD
}
sortbyname "$@"
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