diff scripts/filterFalsePositive.in.pl @ 0:28d1a6f8143f draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/filterFalsePositive.in.pl	Mon Apr 25 13:08:56 2016 -0400
@@ -0,0 +1,39 @@
+#!/share/bin/perl
+use List::Util qw(max min);
+#system("windowBed -a $ARGV[0] -b /home/wangj2/flycommon/all_transposons.dml.rmskCrossmatch.bed -sw -r 1000 -l 0 > tmp");
+#system("windowBed -a $ARGV[0] -b /home/wangj2/flycommon/soo.trnalnpos.map2.sort.bed -sw -r 1000 -l 0 > tmp");
+system("bedtools window -a $ARGV[0] -b $ARGV[1] -sw -r 1000 -l 0 > tmp");
+
+open in,"tmp";
+my %read;
+while(<in>)
+{
+	chomp;
+	split/\t/;
+
+	## if the same tpye of transposons
+	my @loc=map { [/(.*?),(\+|-)(.*)/] } split/;/,$_[4];
+	foreach my $l (@loc)
+	{
+		if($$l[0] eq $_[9])
+		{	
+			## if the same strand of transposons
+			if((($_[5] eq $$l[1]) && ($_[11] eq "-")) || (($_[5] ne $$l[1]) && ($_[11] eq "+")))
+			{
+				## if the fragments of the exists transposons
+				{
+					my $s=max($$l[2],$_[12]);
+					my $e=min(($$l[2]+$_[2]-$_[1]),$_[13]);
+					if($s<$e)
+					{
+						print join("\t",@_[0..5]),"\n" if not exists $read{$_[3]};
+						$read{$_[3]}=1;
+					}
+				}
+			}
+		}
+	}
+}
+close in;
+
+system("rm tmp");