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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified August 6, 2019
Description: Creates a mutant version of a genome.
Usage: mutate.sh in=<input file> out=<output file> id=<identity>
I/O parameters:
in=<file> Input genome.
out=<file> Output mutant genome.
vcf=<file> Output VCF file showing variations added.
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
level; lower compression is faster.
Processing parameters:
subrate=0 Substitution rate, 0 to 1.
indelrate=0 Indel rate, 0 to 1.
maxindel=1 Max indel length.
indelspacing=10 Minimum distance between subsequent indels.
id=1 Target identity, 0 to 1; 1 means 100%.
If this is used it will override subrate and indelrate;
99% of the mutations will be substitutions, and 1% indels.
fraction=1 Genome fraction, 0 to 1; 1 means 100%. A lower fraction
will randomly select that fraction on a per-sequence basis,
possibly incurring one chimeric junction per sequence.
Not compatible with VCF output.
period=-1 If positive, place exactly one mutation every X bases.
prefix= Set this flag to rename the new contigs with this prefix
and a number.
amino=f Treat the input as amino acid sequence.
ploidy=1 Set the ploidy. ploidy>1 allows heterozygous mutations.
This will create one copy of each input sequence per ploidy.
hetrate=0.5 If polyploid, fraction of mutations that are heterozygous.
nohomopolymers=f If true, prevent indels in homopolymers that lead to
ambiguous variant calls. For example, inserting A between
AC or deleting T from TTTT. This is mainly for grading
purposes. It does not fully solve the problem, but greatly
improves concordance (reducing disagreements by 70%).
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.
"
}
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${RAM}m"
}
calcXmx "$@"
mutate() {
local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.MutateGenome $@"
echo $CMD >&2
eval $CMD
}
mutate "$@"
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