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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified September 1, 2016
Description: Filters reads by name.
Usage: filterbyname.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> names=<string,string,string> include=<t/f>
in2 and out2 are for paired reads and are optional.
If input is paired and there is only one output file, it will be written interleaved.
Important! Leading > and @ symbols are NOT part of sequence names; they are part of
the fasta, fastq, and sam specifications. Therefore, this is correct:
names=e.coli_K12
And these are incorrect:
names=>e.coli_K12
names=@e.coli_K12
Parameters:
include=f Set to 'true' to include the filtered names rather than excluding them.
substring=f Allow one name to be a substring of the other, rather than a full match.
f: No substring matching.
t: Bidirectional substring matching.
header: Allow input read headers to be substrings of names in list.
name: Allow names in list to be substrings of input read headers.
prefix=f Allow names to match read header prefixes.
case=t (casesensitive) Match case also.
ow=t (overwrite) Overwrites files that already exist.
app=f (append) Append to files that already exist.
zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
int=f (interleaved) Determines whether INPUT file is considered interleaved.
names= A list of strings or files. The files can have one name per line, or
be a standard read file (fasta, fastq, or sam).
minlen=0 Do not output reads shorter than this.
ths=f (truncateheadersymbol) Ignore a leading @ or > symbol in the names file.
tws=f (truncatewhitespace) Ignore leading or trailing whitespace in the names file.
truncate=f Set both ths and tws at the same time.
Positional parameters:
These optionally allow you to output only a portion of a sequence. Zero-based, inclusive.
Intended for a single sequence and include=t mode.
from=-1 Only print bases starting at this position.
to=-1 Only print bases up to this position.
range= Set from and to with a single flag.
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.
To read from stdin, set 'in=stdin'. The format should be specified with an extension, like 'in=stdin.fq.gz'
To write to stdout, set 'out=stdout'. The format should be specified with an extension, like 'out=stdout.fasta'
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="-Xmx800m"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 800m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
function filterbyname() {
local CMD="java $EA $EOOM $z -cp $CP driver.FilterReadsByName $@"
echo $CMD >&2
eval $CMD
}
filterbyname "$@"
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