--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fimo_gff_to_gff.pl	Thu Mar 03 21:16:32 2016 -0500
@@ -0,0 +1,74 @@
+#! /usr/bin/perl
+
+die "FIMO_GFF_File\tOutput_Path\n" unless $#ARGV == 1;
+my($input, $output) = @ARGV;
+open(IN, "<$input") or die "Can't open $input for reading!\n";
+
+##gff-version 3
+#chr10:265210-265270(-)  fimo    nucleotide_motif        25      36      40.2    +       .       Name=1;ID=1-1-chr10:265210-265270(-);pvalue=9.48e-05;qvalue=0.00885;sequence=ACTTACCCTCAT;
+#chr10:295039-295099(+)  fimo    nucleotide_motif        25      36      55.3    +       .       Name=1;ID=1-1-chr10:295039-295099(+);pvalue=2.97e-06;qvalue=0.00107;sequence=TGTTACCCGTTC;
+#chr10:576747-576807(-)  fimo    nucleotide_motif        25      36      56.2    +       .       Name=1;ID=1-1-chr10:576747-576807(-);pvalue=2.37e-06;qvalue=0.00107;sequence=CGTTACCCGACC;
+
+#chr1        genetrack        .        123950        123970        22        +        .        stddev=0.0
+#chr1        genetrack        .        565745        565765        12        +        .        stddev=0.0
+#chr1        genetrack        .        565793        565813        44        +        .        stddev=0.298065387468
+
+@COORD = ();
+@ID_NUM = ();
+$line = "";
+while($line = <IN>) {
+        chomp($line);
+        next if($line =~ /gff-version/);
+        @array = split(/\t/, $line);
+        @CHR = split(/\:/, $array[0]);
+        @gff_COORD = split(/\(/, $CHR[1]);
+        @START_array = split(/\-/, $gff_COORD[0]);
+        $fimo_DIR = "+";
+        if($gff_COORD[1] =~ "-") { $fimo_DIR = "-"; }
+
+        $DIR = $array[6];
+        $SCORE = $array[5];
+
+        @NAME = split(/\;/, $array[8]);
+        $NEW = 0;
+        for($x = 0; $x <= $#ID_NUM; $x++) {
+                if($ID_NUM[$x] eq $NAME[0]) {
+                        $NEW = 1;
+                        $x = $#ID_NUM + 1;
+                }
+        }
+        if($NEW == 0) { push(@ID_NUM, $NAME[0]); }
+
+        $START = $START_array[0] + $array[3];
+        $STOP = $START_array[0] + $array[4];
+
+        if($fimo_DIR eq "-") {
+                if($DIR eq "+") { $DIR = "-"; }
+                else { $DIR = "+"; }
+        }
+
+        $newline = "$CHR[0]\tfimo\tmotif\t$START\t$STOP\t$SCORE\t$DIR\t.\t$CHR[0]\_$START\_$STOP\_$DIR";
+        $EXISTS = 0;
+        for($x = 0; $x <= $#COORD; $x++) {
+                if($newline eq $COORD[$x]{'line'}) {
+                        $EXISTS = 1;
+                }
+        }
+        if($EXISTS == 0) {
+                push(@COORD, {chr => $CHR[0], start => $START, stop => $STOP, dir => $DIR, score =>$SCORE, id => $NAME[0], line => $newline});
+        }
+}
+close IN;
+@SORT = sort { $$b{'score'} <=> $$a{'score'} } @COORD;
+
+for($x = 0; $x <= $#ID_NUM; $x++) {
+        @FILENAME = split(/\=/, $ID_NUM[$x]);
+        $FILE = "MOTIF$FILENAME[1]";
+        open(OUT, ">$output/$FILE.gff") or die "Can't open $output/$FILE.gff for writing!\n";
+        for($y = 0; $y <= $#SORT; $y++) {
+                if($SORT[$y]{'id'} eq $ID_NUM[$x]) {
+                        print OUT $SORT[$y]{'line'},"\n";
+                }
+        }
+        close OUT;
+}