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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified May 18, 2016
Description: Filters NCBI assembly summaries according to their taxonomy.
The specific files are available here:
ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_genbank.txt
or ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt
ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt
or ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt
Usage: filterassemblysummary.sh in=<input file> out=<output file> tree=<tree file> table=<table file> ids=<numbers> level=<name or number>
Standard parameters:
in=<file> Primary input.
out=<file> Primary output.
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
Processing parameters:
level= Taxonomic level, such as phylum. Filtering will operate on
sequences within the same taxonomic level as specified ids.
reqlevel= Require nodes to have ancestors at these levels. For example,
reqlevel=species,genus would ban nodes that are not defined
at both the species and genus levels.
ids= Comma-delimited list of NCBI numeric IDs.
names= Alternately, a list of names (such as 'Homo sapiens').
Note that spaces need special handling.
include=f 'f' will discard filtered sequences, 't' will keep them.
tree= A taxonomic tree made by TaxTree, such as tree.taxtree.gz.
table= A table translating gi numbers to NCBI taxIDs.
Only needed if gi numbers will be used.
* 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="-Xmx4g"
z2="-Xms4g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 1000m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
filterassemblysummary() {
local CMD="java $EA $EOOM $z -cp $CP driver.FilterAssemblySummary $@"
echo $CMD >&2
eval $CMD
}
filterassemblysummary "$@"
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