--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/cutgff.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,90 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified October 15, 2019
+
+Description:  Cuts out features defined by a gff file, and writes them
+to a new fasta.  Features are output in their sense strand.
+
+Usage:  cutgff.sh in=<fna file> gff=<gff file> out=<fna file>
+
+in= is optional, and gff filenames will be automaitically assumed based on
+the fasta name if not specified.  This allows running on multiple files
+like this:
+
+cutgff.sh types=rRNA out=16S.fa minlen=1440 maxlen=1620 attributes=16S bacteria/*.fna.gz
+
+
+File Parameters:
+in=<file>           Input FNA (fasta) file.
+gff=<file>          Input GFF file (optional).
+out=<file>          Output FNA file.
+
+Other Parameters:
+types=CDS           Types of features to cut.
+invert=false        Invert selection: rather outputting the features,
+                    mask them with Ns in the original sequences.
+attributes=         A comma-delimited list of strings.  If present, one of
+                    these strings must be in the gff line attributes.
+bannedattributes=   A comma-delimited list of banned strings.
+banpartial=t        Ignore lines with 'partial=true' in attributes.
+minlen=1            Ignore lines shorter than this.
+maxlen=2147483647   Ignore lines longer than this.
+renamebytaxid=f     Rename sequences with their taxID.  Input sequences
+                    must be named appropriately, e.g. in NCBI format.
+taxmode=accession   Valid modes are:
+                       accession: Sequence names must start with an accession.
+                       gi:        Seqence names must start with gi|number
+                       taxid:     Sequence names must start with tid|number
+                       header:    Best effort for various header formats.
+requirepresent=t    Crash if a taxID cannot be found for a sequence.
+oneperfile=f        Only output one sequence per file.
+align=f             Align ribosomal sequences to consensus (if available);
+                    discard those with low identity, and flip those
+                    annotated on the wrong strand.
+maxns=-1            If non-negative, ignore features with more than this many
+                    undefined bases (Ns or IUPAC symbols).
+maxnfraction=-1.0   If non-negative, ignore features with more than this
+                    fraction of undefined bases (Ns or IUPAC symbols).
+                    Should be 0.0 to 1.0.
+"
+}
+
+#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="-Xmx200m"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+}
+calcXmx "$@"
+
+gff() {
+	local CMD="java $EA $EOOM $z -cp $CP gff.CutGff $@"
+#	echo $CMD >&2
+	eval $CMD
+}
+
+gff "$@"