diff scripts/excision.clustering.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/excision.clustering.pl	Mon Apr 25 13:08:56 2016 -0400
@@ -0,0 +1,40 @@
+#! /usr/bin/perl
+
+use strict;
+
+my %position=();
+my %names=();
+open (input, "<$ARGV[0]") or die "Can't open $ARGV[0] since $!\n";
+while (my $line=<input>) {
+    chomp($line);
+    my @a=split(/\t/, $line);
+    my @b=split(/\#/, $a[8]);
+
+    if (defined $position{$b[0]}) {
+	my @c=split(/\:/, $position{$b[0]});
+	if (($c[0] eq $a[0])&&($a[1] < $c[1])) {
+	    $position{$b[0]} =~ s/$c[1]/$a[1]/;
+	}
+	if (($c[0] eq $a[0])&&($a[2] > $c[2])) {
+	    $position{$b[0]} =~ s/$c[2]/$a[2]/;
+	}
+	my $transposon=$a[3];
+	if ($names{$b[0]} !~ /$transposon/) {$names{$b[0]}=$names{$b[0]}.",$transposon";}
+    }
+    else {
+	$position{$b[0]}="$a[0]\:$a[1]\:$a[2]";
+	$names{$b[0]}=$a[3];
+    }
+}
+close input;
+
+open (output, ">>temp_for_sort") or die "Can't open temp_for_sort since $!\n";
+while ((my $key, my $value) = each (%position)) {
+    my @z=split(/\:/, $value);
+    print output "$z[0]\t$z[1]\t$z[2]\t$names{$key}\n";
+}
+close output;
+
+system("sort +0 -1 +1n -2 +2n -3 temp_for_sort > sorted");
+system("uniq -c sorted > $ARGV[1]");
+system("rm sorted temp_for_sort");