--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Dotplot_Release/SOFD.pl	Fri Jan 29 09:56:02 2016 -0500
@@ -0,0 +1,112 @@
+#!/usr/bin/perl
+
+# 17/12/2013
+
+if($#ARGV==0){
+	print "This program takes the Saint Output File and produces two matrices.\n";
+	print "One has average spectral counts and the other FDR scores,\n";
+	print "\nusage:\n $0\n-i [csv saint output file]\n-s [FDR cutoff, default=0.01]\n\n";
+	die;
+}
+else{
+	$i=0;
+	$cutoff=0.01;
+        $spec_cutoff=0;
+	while($i<=$#ARGV){
+		if($ARGV[$i] eq '-i'){
+			$i++;
+			$ifile=$ARGV[$i];
+		}
+		elsif($ARGV[$i] eq '-s'){
+			$i++;
+			if($ARGV[$i]>1 || $ARGV[$i]<0){  
+				die "\nFDR cutoff must be between 0 and 1 \n\n";
+			}
+			$cutoff=$ARGV[$i];
+		}
+	        elsif($ARGV[$i] eq '-x'){
+			$i++;
+			if($ARGV[$i]<0){  
+				die "\nAvgSpec cutoff must be > 0 \n\n";
+			}
+			$spec_cutoff=$ARGV[$i];
+		}
+		else{
+			die "\Incorrect program usage\n\n";
+		}
+		$i++;
+	}
+}
+
+$baitn=0, $bait[0]=xxxx, $sig_preysn=0;
+$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]+\t[\d]+\t([\d\.]+)\t[\d]+\t[^\t]+\t[^\t]+\t[^\t]+\t[^\t]+\t[^\t]+\t([^\t]+)\t[^\t]+\t([^\t]+)\t/){
+		if($1 ne $bait[$baitn]){
+			$baitn++;
+			$bait[$baitn]=$1;
+			$preyn[$baitn]=0;
+		}
+		$preyn[$baitn]++;
+		$preys[$baitn][$preyn[$baitn]]=$2;	
+		$avgspec[$baitn][$preyn[$baitn]]=$3;	
+		$saint[$baitn][$preyn[$baitn]]=$4;
+		$fdr[$baitn][$preyn[$baitn]]=$5;
+		if($5 <= $cutoff && $3 >= $spec_cutoff){
+			$check_prey=0;
+			for($i=1; $i<=$sig_preysn; $i++){
+				if($sig_preys[$i] eq $2){
+					$check_prey=1;
+				}
+			}
+			if($check_prey==0){
+				$sig_preysn++;
+				$sig_preys[$sig_preysn]=$2;
+			}
+		}
+	}
+	else{
+	}
+}	
+close(IFILE);
+
+open(SC_FILE, ">SC_data.txt");
+open(FDR_FILE, ">FDR_data.txt");
+
+for($i=1; $i<=$baitn; $i++){
+	print SC_FILE "\t$bait[$i]";
+	print FDR_FILE "\t$bait[$i]";
+}
+print SC_FILE "\n";
+print FDR_FILE "\n";
+for($i=1; $i<=$sig_preysn; $i++){
+	print SC_FILE "$sig_preys[$i]";
+	print FDR_FILE "$sig_preys[$i]";
+	for($j=1; $j<=$baitn; $j++){
+		$krem=0;
+		for($k=1; $k<=$preyn[$j]; $k++){;
+			if($preys[$j][$k] eq $sig_preys[$i]){
+				$krem=$k;
+				last;
+			}
+		}
+		if($krem != 0){
+			print SC_FILE "\t$avgspec[$j][$krem]";
+			print FDR_FILE "\t$fdr[$j][$krem]";
+		}
+		else{
+			print SC_FILE "\t0";
+			print FDR_FILE "\t1";
+		}
+	}
+	print SC_FILE "\n";
+	print FDR_FILE "\n";
+}
+close(SC_FILE);
+close(FDR_FILE);
+