diff scripts/summarize_excision.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/summarize_excision.pl	Mon Apr 25 13:08:56 2016 -0400
@@ -0,0 +1,55 @@
+#! /usr/bin/perl
+
+use strict;
+
+my @files=<*.excision.cluster.*.refined.bp>;
+foreach my $file (@files) {
+    my $rfsp=$file.".refsup";
+    my $count=$file;
+    my $title=$file;
+    $count =~ s/.refined.bp//;
+    $title =~ s/excision/absence/;
+    $title =~ s/.cluster.rpmk//;
+    $title .= ".summary";
+	
+    open (input, "<$file") or die "Can't open $file since $!\n";
+    open (input1, "<$count") or die "Can't open $count since $!\n";
+    open (input2, "<$rfsp") or die "Can't open $rfsp since $!\n";
+    open (output, ">>$title") or die "Can't open $title since $!\n";
+    my $header=<input>; 
+    chomp($header);
+    print output "$header\tVariant\tReference\tFrequency\n";
+    while (my $line=<input>) {
+	chomp($line);
+	my @a=split(/\t/, $line);
+	my $line1=<input1>;
+	my $line2=<input2>;
+	chomp($line1);
+	chomp($line2);
+	my @b=split(/\s+/, $line1);
+	my @c=split(/\t/, $line2);
+
+	my $variant=$b[1];
+	my @x=split(/\:/, $a[4]);
+	my @y=split(/\:/, $a[5]);
+	if ($a[4] =~ /\,/) {
+	    my @m=split(/\,/, $x[1]);
+	    $variant += $m[0]+$x[2];
+	}
+	else {$variant += $x[1];}
+	if ($a[5] =~ /\,/) {
+	    my @n=split(/\,/, $y[1]);
+	    $variant += $n[0]+$y[2];
+	}
+	else {$variant += $y[1];}
+	my $ratio=sprintf("%.4f", ($variant*2)/($variant*2+$c[6]));
+	
+	$line =~ s/:\d+//g;
+	print output "$line\t$variant\t$c[6]\t$ratio\n";
+    }
+    
+    close input;
+    close input1;
+    close input2;
+    close output;
+}