--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chromeister/bin/index_chromeister.sh	Wed Dec 12 07:18:40 2018 -0500
@@ -0,0 +1,80 @@
+#!/usr/bin/env bash
+DIR=$1
+FASTAS1=$3
+FASTAS2=$4
+OUT=$2
+
+echo "Computing index CSV..." > index.csv.temp
+
+while [ "$(find . -size 0 | wc -l)" -ne 0 ]; do
+        sleep 10s
+done
+
+
+EXT="mat"
+EXTSCORE="scr.txt"
+EXTGENERAL=".fa.fasta"
+
+
+
+if [ $# != 4 ]; then
+	echo "***ERROR*** Use: $0 <directory> <out> <fastas_directory_1> <fastas_directory_2>"
+	exit -1
+fi
+
+rm $DIR/*.log
+
+for i in $DIR/*.scr; do mv $i $i.txt; done
+
+rm $OUT
+
+for elem in $(ls -d $DIR/*.$EXT | awk -F "/" '{print $NF}' | awk -F ".$EXT" '{print $1}')
+do
+	IFS='-', read -a splits <<< "$elem"
+	IFS='.', read -a getnum <<< "$elem"
+
+	scorepath=$(basename $elem .mat).$EXTSCORE
+
+	sed -i "/X.*/d" $DIR/$scorepath
+	sed -i "s/\[1\]//g" $DIR/$scorepath
+
+	score=$( head -1  $DIR/$scorepath)
+
+	file1=${splits[0]}
+	file2=$(basename ${splits[1]} .mat)
+
+	ID1=$(head -1 $FASTAS1/$file1)
+	ID2=$(head -1 $FASTAS2/$file2)
+
+	
+	#scorepath="$(basename $elem .mat).$EXTSCORE"
+	#score="$(head -1 $DIR/$scorepath)"
+
+	counter=0
+	numX=0
+	numY=0
+	for i in "${getnum[@]}" 
+	do
+		counter=`expr $counter + 1`
+		if [ "$numX" -eq 0 ] && [ "$i" == "chromosome" ]; then
+			numX=$counter
+			continue
+		fi
+		if [ "$numX" -ne 0 ] && [ "$i" == "chromosome" ]; then
+			numY=$counter
+		fi
+
+	done
+
+
+	echo "$(basename ${splits[0]} $EXTGENERAL),$(basename ${splits[1]} ${EXTGENERAL}.mat),$ID1,$ID2,$elem.$EXT.filt.png,${getnum[${numX}]},${getnum[${numY}]},$score" >> $OUT
+
+done
+
+sort -k5,5n -k6,6n -o $OUT $OUT 
+
+
+sed -i '1iSpX, SpY, IDX, IDY, IMG, CHNumberX, CHNumberY, Score' $OUT
+
+rm index.csv.temp
+