--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Tools/First_version/sorting_first_galaxy.pl	Mon Sep 05 05:53:08 2016 -0400
@@ -0,0 +1,88 @@
+#!/usr/bin/perl -w
+
+$|=1;
+use warnings;
+use strict;
+
+my $line;
+my @cols;
+my %hash1;
+my %hash2;
+my @list1;
+my @list2;
+my $gene;
+my $pos1;
+my $n;
+my $index;
+my $position;
+my $scalar;
+my $TF;
+
+if(@ARGV < 2){
+print "\nUsage: sorting_promoters_by_first_position.pl fimo.gff fimo-position-sorted.gff e\n\n";
+exit(0);
+}
+
+my $counter=0;
+open(FIMO, "<$ARGV[0]") ||
+    die "File '$ARGV[0]' not found\n";
+open(OUTPUT, ">$ARGV[1]") ||
+    die "File '>$ARGV[1]' not found\n";
+    
+while (<FIMO>) {
+    $line=$_;
+    chomp $line;
+    @cols=split;
+    
+    if ($line=~/^#/){
+        printf OUTPUT "%s\n", $line;
+        $counter++;
+    }
+    else {
+        $gene=substr $cols[0],0,21;
+        $pos1 = $cols[3];
+        $TF= substr $cols[8],5,8;
+        $scalar= scalar @list1;
+        if (not exists $hash1{$gene}{$TF} and not $scalar == 0) {
+            $n= scalar @list1;
+            my @list_pos_sorted= sort { $list1[$a] <=> $list1[$b] } 0..($n - 1);
+            for (my $i=0; $i <(scalar @list_pos_sorted); $i++){
+                $index=$list_pos_sorted[$i];
+                $position = $list1[$index];
+                printf OUTPUT "%s\n", $hash2{$position};
+                #print $list2[$index], "\n";
+                $counter++;
+            }
+        }
+        if (not exists $hash1{$gene}{$TF}) {
+           %hash1=();
+           %hash2=();
+           @list1=();
+           @list2=();
+           $hash1{$gene}{$TF}=1;
+           $hash2{$pos1}=$line;
+           push @list1, $pos1;
+           push @list2, $line;       
+        }
+       
+        elsif (exists $hash1{$gene}{$TF}) {
+           $hash2{$pos1}=$line;
+           push @list1, $pos1;
+           push @list2, $line;
+        }
+        
+        
+    }
+  
+}
+
+$n= scalar @list1;
+my @list_pos_sorted= sort { $list1[$a] <=> $list1[$b] } 0..($n - 1);
+            for (my $i=0; $i <(scalar @list_pos_sorted); $i++){
+                $index=$list_pos_sorted[$i];
+                $position = $list1[$index];
+                printf OUTPUT "%s\n", $hash2{$position};
+                #print $list2[$index], "\n";
+                $counter++;
+            }
+#print $counter;