diff chromeister/bin/run_and_plot_chromeister.sh @ 0:7fdf47a0bae8 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chromeister/bin/run_and_plot_chromeister.sh	Wed Dec 12 07:18:40 2018 -0500
@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+G1=$1
+G2=$2
+KMER=$3
+DIM=$4
+
+
+FILE1=$(basename $G1)
+FILE2=$(basename $G2)
+
+BINDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+
+if [ $# -lt 4 ]; then
+        echo "***ERROR*** Use: $0 <G1> <G2> <KMER> <DIMENSION>"
+        exit -1
+fi
+
+
+
+(time $BINDIR/CHROMEISTER -query $G1 -db $G2 -kmer $KMER -out $FILE1-$FILE2.mat -dimension $DIM) &> $FILE1-$FILE2.log
+(Rscript $BINDIR/compute_score.R $FILE1-$FILE2.mat $DIM) &> $FILE1-$FILE2.scr.txt
+
+#$BINDIR/plot.R $FILE1-$FILE2.mat
+
+
+#rm $FILE1-$FILE2.mat