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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified February 17, 2015
Description: Translates nucleotide sequences to all 6 amino acid frames,
or amino acids to a canonical nucleotide representation.
Input may be fasta or fastq, compressed or uncompressed.
Usage: translate6frames.sh in=<input file> out=<output file>
See also: callgenes.sh
Optional parameters (and their defaults)
Input parameters:
in=<file> Main input. in=stdin.fa will pipe from stdin.
in2=<file> Input for 2nd read of pairs in a different file.
int=auto (interleaved) t/f overrides interleaved autodetection.
qin=auto Input quality offset: 33 (Sanger), 64, or auto.
aain=f False if input is nucleotides, true for amino acids.
reads=-1 If positive, quit after processing X reads or pairs.
Output parameters:
out=<file> Write output here. 'out=stdout.fa' goes to standard out.
out2=<file> Use this to write 2nd read of pairs to a different file.
overwrite=t (ow) Grant permission to overwrite files.
append=f Append to existing files.
ziplevel=2 (zl) Compression level; 1 (min) through 9 (max).
fastawrap=80 Length of lines in fasta output.
qout=auto Output quality offset: 33 (Sanger), 64, or auto.
aaout=t False to output nucleotides, true for amino acids.
tag=t Tag read id with the frame, adding e.g. ' fr1'
frames=6 Only print this many frames.
If you already know the sense, set 'frames=3'.
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 [[ $set == 1 ]]; then
return
fi
freeRam 2000m 42
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
translate6frames() {
local CMD="java $EA $EOOM $z -cp $CP jgi.TranslateSixFrames $@"
echo $CMD >&2
eval $CMD
}
translate6frames "$@"
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