--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/change_o/define_clones.sh	Fri Feb 19 15:10:54 2021 +0000
@@ -0,0 +1,39 @@
+#!/bin/bash
+dir="$(cd "$(dirname "$0")" && pwd)"
+
+#define_clones.sh $input $noparse $scores $regions $out_file
+
+type=$1
+input=$2
+
+mkdir -p $PWD/outdir
+
+cp $input $PWD/input.tab #file has to have a ".tab" extension
+
+if [ "bygroup" == "$type" ] ; then	
+	mode=$3
+	act=$4
+	model=$5
+	norm=$6
+	sym=$7
+	link=$8
+	dist=$9
+	output=${10}
+	output2=${11}
+	
+	DefineClones.py -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link
+	
+	Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
+else
+	method=$3
+	output=$4
+	output2=$5
+	
+	DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
+	
+	Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
+fi
+
+cp $PWD/outdir/output_clone-pass.tab $output
+
+rm -rf $PWD/outdir/