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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified Jan 7, 2020
Description: Prints the full taxonomy of a string.
String may be a gi number, NCBI taxID, or Latin name.
An NCBI identifier should just be a number or ncbi|number.
A gi number should be gi|number.
Please read bbmap/docs/guides/TaxonomyGuide.txt for more information.
Not: It is more convenient to use taxonomy.jgi-psf.org.
Usage: taxonomy.sh tree=<tree file> <identifier>
Alternate usage: taxonomy.sh tree=<tree file> in=<file>
Usage examples:
taxonomy.sh tree=tree.taxtree.gz homo_sapiens canis_lupus 9606
taxonomy.sh tree=tree.taxtree.gz gi=gitable.int1.d.gz in=refseq.fasta
Processing parameters:
in=<file> A file containing named sequences, or just the names.
out=<file> Output file. If blank, use stdout.
tree=<file> Specify a TaxTree file like tree.taxtree.gz.
On Genepool, use 'auto'.
gi=<file> Specify a gitable file like gitable.int1d.gz. Only needed
if gi numbers will be used. On Genepool, use 'auto'.
accession= Specify one or more comma-delimited NCBI accession to taxid
files. Only needed if accesions will be used; requires ~45GB
of memory. On Genepool, use 'auto'.
level=null Set to a taxonomic level like phylum to just print that level.
minlevel=-1 For multi-level printing, do not print levels below this.
maxlevel=life For multi-level printing, do not print levels above this.
silva=f Parse headers using Silva or semicolon-delimited syntax.
taxpath=auto Set the path to taxonomy files; auto only works at NERSC.
Parameters without an '=' symbol will be considered organism identifiers.
* Note *
Tree and table files are in /global/projectb/sandbox/gaag/bbtools/tax
For non-Genepool users, or to make new ones, use taxtree.sh and gitable.sh
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="-Xmx8g"
z2="-Xms8g"
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${RAM}m"
}
calcXmx "$@"
taxonomy() {
local CMD="java $EA $EOOM $z -cp $CP tax.PrintTaxonomy $@"
echo $CMD >&2
eval $CMD
}
taxonomy "$@"
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