diff bin/vslz.pl @ 1:adc0f7765d85 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/vslz.pl	Thu Sep 07 15:06:58 2017 -0400
@@ -0,0 +1,46 @@
+use strict;
+exit;
+
+my %config=do "$ENV{HOME}/.SpliceTrap.pl.ini";
+my $SrcFolder=$config{SrcFolder};
+
+my $BedFileName=$SrcFolder."/db/TXdb.1101.bed";
+my $RatioFileName=$ARGV[0];
+my $BedFileOutName=$ARGV[1];
+my %Ratios;
+
+open(RatioFile, $RatioFileName);
+
+while(my $RatioLine=<RatioFile>)
+{
+	chomp($RatioLine);
+	my @array=split("\t",$RatioLine);
+	$Ratios{$array[0]}=$array[2] if $array[14] eq "passed";
+}
+
+close(RatioFile);
+
+open(BedFile, $BedFileName);
+open(BedFileOut,">".$BedFileOutName.".bed");
+print BedFileOut "track name=$BedFileOutName discription=$BedFileOutName useScore=1\n";
+while(my $BedLine=<BedFile>)
+{
+	my @array=split("\t",$BedLine);
+	$array[3]=~/^(\S*)\[([LS])\]/;
+	my $id=$1;
+	my $LS=$2;
+	#print $LS,"\n";
+	next if not exists $Ratios{$id};
+	$array[4]=$Ratios{$id};
+	$array[4]=1-$Ratios{$id} if( $LS eq 'S');
+
+	$array[4]=sprintf("%.0f",$array[4]*1000);
+	for (my $i=0;$i<@array; $i++)
+	{
+		print BedFileOut $array[$i];
+		print BedFileOut "\t" if $i<scalar(@array)-1;
+	}
+	#print BedFileOut "\n";
+}
+close(BedFileOut);
+close(BedFile);