comparison nibls.pl @ 19:e0884a4b996b draft

Uploaded

18:22d79320085c

#	my $length1=$end-$start+1;
#	if ($length1>30) {
#		$length1=40;
#	}
	my $total;
	foreach (0..$#data) {
		$total+=$_;
	}
	push @data,$total;
#	push @data,$length1;
#	if (defined $molecules{$chr}{$start}{$end}{$strand}) {
#		my @old_data=split(/;/,$molecules{$chr}{$start}{$end}{$strand});

		$node =~ m/^(\S+):(\d+):(\d+)$/;
		my $c=$1;
		my $s=$2;
		my $e=$3;
		my @data;
		foreach my $str (keys %{$molecules{$c}{$s}{$e}}) {
			push @tag,($s.",".$e.",".$str);
			@data=split(/;/,$molecules{$c}{$s}{$e}{$str});
#			for (my $i=0;$i<$#old_data ;$i++) {
#				$data[$i]+=$old_data[$i];
#			}
			my $length=$e-$s+1;
			if ($length>30) {

		$chr = $c;
		$start = $s if $s < $start;
		$end = $e if $e > $end;
	}
	my $tag=join";",@tag;
	
	my ($max_length,$max_p,@cluster_exp)=Max_length(\@sample);
	if ($max_length==40) {
		$max_length="\>30";
	}
	my $cluster_exp=join"\t",@cluster_exp;
	my $gff = $chr."\:$start\-$end\t".$max_length."nt\t".$max_p."\t" . $cluster_exp;
	print CLUSTER "$chr\:$start\-$end\t$max_length"."nt\t$max_p\t$tag\n";
	print OUT $gff, "\n";  
}

sub Max_length{
	my @exp=@{$_[0]};

19:e0884a4b996b

#	my $length1=$end-$start+1;
#	if ($length1>30) {
#		$length1=40;
#	}
	my $total;
	for (my $s=0;$s<@data ;$s++) {
		$total+=$data[$s];
	}
	push @data,$total;
#	push @data,$length1;
#	if (defined $molecules{$chr}{$start}{$end}{$strand}) {
#		my @old_data=split(/;/,$molecules{$chr}{$start}{$end}{$strand});

		$node =~ m/^(\S+):(\d+):(\d+)$/;
		my $c=$1;
		my $s=$2;
		my $e=$3;
	#	my @data;
		foreach my $str (keys %{$molecules{$c}{$s}{$e}}) {
			my @data=split(/;/,$molecules{$c}{$s}{$e}{$str});
			push @tag,($s.",".$e.",".$str.",".$data[-1]);
#			for (my $i=0;$i<$#old_data ;$i++) {
#				$data[$i]+=$old_data[$i];
#			}
			my $length=$e-$s+1;
			if ($length>30) {

		$chr = $c;
		$start = $s if $s < $start;
		$end = $e if $e > $end;
	}
	my $tag=join";",@tag;
	my $tag_number=@tag;
	my ($max_length,$max_p,@cluster_exp)=Max_length(\@sample);
	if ($max_length==40) {
		$max_length="\>30";
	}
	my $cluster_exp=join"\t",@cluster_exp;
	my $gff = $chr."\:$start\-$end\t".$max_length."nt\t".$max_p."\t" . $cluster_exp;
	print CLUSTER "$chr\:$start\-$end\t$max_length"."nt\t$max_p\t$tag_number\t$tag\n";
	print OUT $gff, "\n";  
}

sub Max_length{
	my @exp=@{$_[0]};