Mercurial > repos > greg > fimo_gff_to_gff

changeset 1:063d97ffda39 draft

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Uploaded
author greg
date Fri, 04 Mar 2016 15:31:45 -0500
parents 48d424adfaef
children 18c06791c675
files fimo_gff_to_gff.pl
diffstat 1 files changed, 24 insertions(+), 24 deletions(-) [+]
line wrap: on
line diff
--- a/fimo_gff_to_gff.pl	Thu Mar 03 21:16:32 2016 -0500
+++ b/fimo_gff_to_gff.pl	Fri Mar 04 15:31:45 2016 -0500
@@ -9,27 +9,27 @@
 #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
+#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($line);
+	chomp($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 = "-"; }
+	@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]);
+	@NAME = split(/\;/, $array[8]);
         $NEW = 0;
         for($x = 0; $x <= $#ID_NUM; $x++) {
                 if($ID_NUM[$x] eq $NAME[0]) {
@@ -39,13 +39,13 @@
         }
         if($NEW == 0) { push(@ID_NUM, $NAME[0]); }
 
-        $START = $START_array[0] + $array[3];
-        $STOP = $START_array[0] + $array[4];
+        $START = $START_array[0] + $array[3] - 1;
+        $STOP = $START_array[0] + $array[4] - 1;
 
-        if($fimo_DIR eq "-") {
-                if($DIR eq "+") { $DIR = "-"; }
-                else { $DIR = "+"; }
-        }
+	if($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;
@@ -62,13 +62,13 @@
 @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;
+	@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;
 }