comparison scripts/make.bp.bed.pl @ 21:9672fe07a232 draft default tip

planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty

20:6e02b9179a24

	my $j=$i+1;
	my $k=$i+2;
	my $l=$i+3;
	system("cut -f7,4,6,$j,$k,$l $ARGV[0] > temp");
	open (input, "<temp") or die "Can't open temp since $!\n";
	open (output, ">>$name.insertion.bp.bed") or die "Can't open $name.insertion.bp.bed since $!\n";
	my $header=<input>;
	while (my $line=<input>) {
	    chomp($line);
	    my @b=split(/\t/, $line);
	    if (($b[4] ne "0")||($b[5] ne "0")) {
		my @c=split(/\:/, $b[2]);
		my @d=split(/\./, $c[1]);
		if ($d[0] > $d[1]) {
		    my $temp=$d[0];
		    $d[0]=$d[1];
		    $d[1]=$temp;
		}
		my $lower=$d[0];
		my $upper=$d[1];
	        if (($lower >= 0) && ($upper >= 0)) {
		   print output "$c[0]\t$lower\t$upper\t$b[0]\t$b[1]\t$b[3]\t$b[4]\t$b[5]\n";
	        }
		$chrs{$c[0]}=1;
	    }
	}
	close input;
	close output;

		close input;
		close output;
	    }
	    
	    if (-s "tmp2") {
		system("bedtools subtract -a tmp -b tmp2 -f 1.0 > tmp3");
		open (input, "<tmp3") or die "Can't open tmp3 since $!\n";
		open (output, ">$name.insertion.bp.bed") or die "Can't open $name.insertion.bp.bed since $!\n";
		while (my $line=<input>) {
		    chomp($line);
		    my @a=split(/\t/, $line);
		    my $direction="sense";
		    if ($a[5] eq "-") {$direction="antisense";}
		    my $chr_num=$a[0];
		    $chr_num =~ s/chr//;
		    if (($chrs{$a[0]} == 1) && (! defined $chrs{$chr_num})) {$chr_num=$a[0];}
		    print output "$chr_num\t$a[1]\t$a[2]\t$a[3]\t$direction\t$a[6]\t$a[7]\t$a[8]\n";
		}
		close input;
		close output;
	    }
	}

	system("rm tmp*");

    }
}
	

21:9672fe07a232

	my $j=$i+1;
	my $k=$i+2;
	my $l=$i+3;
	system("cut -f7,4,6,$j,$k,$l $ARGV[0] > temp");
	open (input, "<temp") or die "Can't open temp since $!\n";
	open (output, ">$name.insertion.bp.bed") or die "Can't open $name.insertion.bp.bed since $!\n";
	my $header=<input>;
	while (my $line=<input>) {
	    chomp($line);
	    my @b=split(/\t/, $line);
	    if (($b[4] ne "0")||($b[5] ne "0")) {
		my @c=split(/\:/, $b[2]);
		my @d=split(/\./, $c[1]);
		if ($c[0] eq "P") {next;}
		if ($d[0] > $d[1]) {
		    my $temp=$d[0];
		    $d[0]=$d[1];
		    $d[1]=$temp;
		}
		my $lower=$d[0];
		my $upper=$d[1];
		if (($lower >= 0) && ($upper >= 0)) {
		    print output "$c[0]\t$lower\t$upper\t$b[0]\t$b[1]\t$b[3]\t$b[4]\t$b[5]\n";
		}
		$chrs{$c[0]}=1;
	    }
	}
	close input;
	close output;

		close input;
		close output;
	    }
	    
	    if (-s "tmp2") {
		my %to_filter=();
		open (input, "<tmp2") or die "Can't open tmp2 since $!\n";
		while (my $line=<input>) {
		    chomp($line);
		    my @a=split(/\t/, $line);
		    $to_filter{"$a[0]\:$a[1]\:$a[2]\:$a[3]\:$a[5]"}=1;
		}
		close input;
		open (input, "<tmp") or die "Can't open tmp since $!\n";
		open (output, ">$name.insertion.bp.bed") or die "Can't open $name.insertion.bp.bed since $!\n";
		while (my $line=<input>) {
		    chomp($line);
		    my @a=split(/\t/, $line);
		    if (!defined $to_filter{"$a[0]\:$a[1]\:$a[2]\:$a[3]\:$a[5]"}) {
			my $direction="sense";
			if ($a[5] eq "-") {$direction="antisense";}
			my $chr_num=$a[0];
			$chr_num =~ s/chr//;
			if (($chrs{$a[0]} == 1) && (! defined $chrs{$chr_num})) {$chr_num=$a[0];}
			print output "$chr_num\t$a[1]\t$a[2]\t$a[3]\t$direction\t$a[6]\t$a[7]\t$a[8]\n";
		    }
		}
		close input;
		close output;
	    }

	    system("rm tmp*");

	}

    }
}