1#!/usr/local/bin/bash 2 3usage(){ 4echo " 5Written by Brian Bushnell 6Last modified November 7, 2019 7 8Description: Creates a blacklist sketch from common kmers, 9which occur in at least X different sequences or taxa. 10Please read bbmap/docs/guides/BBSketchGuide.txt for more information. 11 12Usage: sketchblacklist.sh in=<fasta file> out=<sketch file> 13 14Standard parameters: 15in=<file> A fasta file containing one or more sequences. 16out=<file> Output filename. 17mintaxcount=100 Sketch kmers occuring in at least this many taxa. 18k=31 Kmer length, 1-32. To maximize sensitivity and 19 specificity, dual kmer lengths may be used: k=31,24 20mode=sequence Possible modes: 21 sequence: Count kmers once per sequence. 22 taxa: Count kmers once per taxonomic unit. 23name= Set the blacklist sketch name. 24delta=t Delta-compress sketches. 25a48=t Encode sketches as ASCII-48 rather than hex. 26amino=f Amino-acid mode. 27entropy=0.66 Ignore sequence with entropy below this value. 28keyfraction=0.16 Smaller values reduce blacklist size by ignoring a 29 a fraction of the key space. Range: 0.0001-0.5. 30 31Taxonomy-specific flags: 32tree= Specify a taxtree file. On Genepool, use 'auto'. 33gi= Specify a gitable file. On Genepool, use 'auto'. 34accession= Specify one or more comma-delimited NCBI accession to 35 taxid files. On Genepool, use 'auto'. 36taxlevel=subspecies Taxa hits below this rank will be promoted and merged 37 with others. 38prefilter=t Use a bloom filter to ignore low-count kmers. 39prepasses=2 Number of prefilter passes. 40prehashes=2 Number of prefilter hashes. 41prebits=-1 Manually override number of prefilter cell bits. 42tossjunk=t For taxa mode, discard taxonomically uninformative 43 sequences. This includes sequences with no taxid, 44 with a tax level NO_RANK, of parent taxid of LIFE. 45silva=f Parse headers using Silva or semicolon-delimited syntax. 46 47Java Parameters: 48-Xmx This will set Java's memory usage, overriding autodetection. 49 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 50 The max is typically 85% of physical memory. 51-eoom This flag will cause the process to exit if an 52 out-of-memory exception occurs. Requires Java 8u92+. 53-da Disable assertions. 54 55For more detailed information, please read /bbmap/docs/guides/BBSketchGuide.txt. 56Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 57" 58} 59 60#This block allows symlinked shellscripts to correctly set classpath. 61pushd . > /dev/null 62DIR="${BASH_SOURCE[0]}" 63while [ -h "$DIR" ]; do 64 cd "$(dirname "$DIR")" 65 DIR="$(readlink "$(basename "$DIR")")" 66done 67cd "$(dirname "$DIR")" 68DIR="$(pwd)/" 69popd > /dev/null 70 71#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" 72CP="$DIR""current/" 73 74z="-Xmx4g" 75z2="-Xms4g" 76set=0 77 78if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then 79 usage 80 exit 81fi 82 83calcXmx () { 84 source "$DIR""/calcmem.sh" 85 setEnvironment 86 parseXmx "$@" 87 if [[ $set == 1 ]]; then 88 return 89 fi 90 freeRam 4000m 84 91 z="-Xmx${RAM}m" 92 z2="-Xms${RAM}m" 93} 94calcXmx "$@" 95 96sketchblacklist() { 97 local CMD="java $EA $EOOM $z $z2 -cp $CP sketch.BlacklistMaker $@" 98 echo $CMD >&2 99 eval $CMD 100} 101 102sketchblacklist "$@" 103