diff scripts/get_class.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/get_class.pl	Mon Apr 25 13:08:56 2016 -0400
@@ -0,0 +1,45 @@
+#!/share/bin/perl
+
+# chr2L   19384   20049   FBgn0001283_jockey      wXh24,-1;harwich,-8,+5;whXw21,-4,+1;whXw14,-5;wXh14,+2; +-      sense   chr2L:19562.19645
+
+my @sample=("$ARGV[1]");
+
+print "chr\tstart\tend\ttransposonName\tstrand\ttransposonStrand\tbreak\tclass";
+print "\t$_\_class\t$_\_plus\t$_\_minus" foreach @sample;
+print "\n";
+open in,$ARGV[0];
+while(<in>)
+{
+	chomp;
+	my($chrom,$start,$end,$transposonName,$class,$strand,$transposonStrand,$break)=split/\t/;
+	my %classCounts;
+	my ($tcplus,$tcminus)=(0,0);
+	foreach $s (split/;/,$class)
+	{
+		my ($name,@counts)=split/,/,$s;
+		foreach my $c (@counts)
+		{
+			my $strand=($c>0)?"+":"-";
+			$classCounts{$name}{$strand}=$c;
+			$tcplus+=$c if $c>0;
+			$tcminus+=$c if $c<0;
+		}
+	}
+	print "$chrom\t$start\t$end\t$transposonName\t$strand\t$transposonStrand\t$break";
+	print "\t1p1" if $tcplus>0 && $tcminus<0;
+	print "\t2p" if ($tcplus>1 && $tcminus==0) || ($tcplus==0 && $tcminus<-1);
+	print "\tsingleton" if ($tcplus<=1 && $tcminus==0 && $tcplus>0) || ($tcplus==0 && $tcminus>=-1 && $tcminus<0);
+	print "\tNone" if ($tcminus==0 && $tcplus==0);
+	foreach my $s (@sample)
+	{
+		$classCounts{$s}{"+"}=0 if not exists $classCounts{$s}{"+"};
+		$classCounts{$s}{"-"}=0 if not exists $classCounts{$s}{"-"};
+		print "\t1p1" if $classCounts{$s}{"+"}>0 && $classCounts{$s}{"-"}<0;
+		print "\t2p" if ($classCounts{$s}{"+"}>1 && $classCounts{$s}{"-"}==0) || ($classCounts{$s}{"+"}==0 && $classCounts{$s}{"-"}<-1);
+		print "\tsingleton" if ($classCounts{$s}{"+"}<=1 && $classCounts{$s}{"-"}==0 && $classCounts{$s}{"+"}>0) || ($classCounts{$s}{"+"}==0 && $classCounts{$s}{"-"}>=-1 && $classCounts{$s}{"-"}<0);
+		print "\tNone" if $classCounts{$s}{"+"}==0 && $classCounts{$s}{"-"}==0;
+		print "\t",$classCounts{$s}{"+"},"\t",$classCounts{$s}{"-"};
+	}
+	print "\n";
+}
+close in;