--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Dotplot_Release/SaintConvert.pl	Fri Jan 29 09:56:02 2016 -0500
@@ -0,0 +1,52 @@
+#!/usr/bin/perl
+
+# 17/12/2013
+
+if($#ARGV==0){
+	print "This program takes non-SaintExpress formatted data and converts it to look like it.\n";
+	print "\nusage:\n $0\n-i [csv saint output file]\n\n";
+	die;
+}
+else{
+	$i=0;
+	while($i<=$#ARGV){
+		if($ARGV[$i] eq '-i'){
+			$i++;
+			$ifile=$ARGV[$i];
+		}
+		else{
+			die "\Incorrect program usage\n\n";
+		}
+		$i++;
+	}
+}
+
+$i=0;
+$file='';
+open(IFILE,"<$ifile") || die "$ifile can't be opened: $!";
+{ local $/=undef;  $file=<IFILE>; }
+@lines=split /[\r\n]+/, $file;
+foreach $line (@lines) {
+   	if($line =~ /^Bait/){
+	}
+	elsif($line =~ /^([^\t]+)\t([^\t]+)\t([^\t]+)\t([^\t]+)/){
+		$bait[$i]=$1;
+		$prey[$i]=$2;
+		$spec[$i]=$3;
+		$fdr[$i]=$4;
+		$i++;
+	}
+	else{
+	}
+}	
+close(IFILE);
+$line_count=$i;
+
+open(OFILE, ">mockSaintExpress.txt");
+print OFILE "Bait\tPrey\tPreyGene\tSpec\tSpecSum\tAvgSpec\tNumReplicates\tctrlCounts\tAvgP\tMaxP\tTopoAvgP\tTopoMaxP\tSaintScore\tFoldChange\tBFDR\tboosted_by\n";
+
+for($i=0; $i<$line_count; $i++){
+	print OFILE "$bait[$i]\t111\t$prey[$i]\t111\t111\t$spec[$i]\t111\t111\t111\t111\t111\t111\t111\t111\t$fdr[$i]\t111\n";
+}
+close(OFILE);
+