comparison scripts/pickSoftClipping.over.pl @ 21:9672fe07a232 draft default tip

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

20:6e02b9179a24

    my $upper=$a[4]+100;
    my $chr_num=$a[2];
    $chr_num =~ s/chr//;
    if (($chrs{$a[2]} == 1) && (! defined $chrs{$chr_num})) {$chr_num=$a[2];}
    system("samtools view -bu $title $chr_num\:$lower\-$upper > temp.bam");
    system("samtools view -Xf 0x2 temp.bam > temp.sam");

    my $leftseq="";
    my $rightseq="";

    my $ll=$a[3]-150;

    while(<in>)
    {
	chomp;
	my @f=split/\t/,$_,12;
	## read number 1 or 2
	my ($rnum)=$f[1]=~/(\d)$/;
	
	## XT:A:* 
	my ($xt)=$f[11]=~/XT:A:(.)/;

	my $CIGAR=$f[5];

            my $coor=-10;
	    my $overcoor=-10;
            my $strand="";
	    my @z=split(/M/, $f[5]);

            if (($f[5]=~/S$/)&&($f[1]=~/r/))
            {
		my (@cigar_m)=$f[5]=~/(\d+)M/g;
                my (@cigar_d)=$f[5]=~/(\d+)D/g;
                my (@cigar_s)=$f[5]=~/(\d+)S/g;
                my (@cigar_i)=$f[5]=~/(\d+)I/g;

#		    print "$clipseq\t$rightseq\t$overcoor\t";
		    if ($overcoor > -1) {$overcoor += ($a[4] - 149);}
		}
#		print "\n";
            }
            elsif (($f[1]=~/R/)&&($z[0]=~/S/)) {
		$coor=$f[3]; $strand="+";
		my (@clipped)=$z[0]=~/(\d+)S/g;
                my $cliplen=sum(@clipped);
#		print "$f[0]\n";
#		print "$cliplen\t";

21:9672fe07a232

    my $upper=$a[4]+100;
    my $chr_num=$a[2];
    $chr_num =~ s/chr//;
    if (($chrs{$a[2]} == 1) && (! defined $chrs{$chr_num})) {$chr_num=$a[2];}
    system("samtools view -bu $title $chr_num\:$lower\-$upper > temp.bam");
    system("samtools view -f 0x2 temp.bam > temp.sam");

    my $leftseq="";
    my $rightseq="";

    my $ll=$a[3]-150;

    while(<in>)
    {
	chomp;
	my @f=split/\t/,$_,12;
	## read number 1 or 2
	#my ($rnum)=$f[1]=~/(\d)$/;
        my $rnum=1;
        if (($f[1] & 128) == 128) {$rnum=2;}
	
	## XT:A:* 
	my ($xt)=$f[11]=~/XT:A:(.)/;

	my $CIGAR=$f[5];

            my $coor=-10;
	    my $overcoor=-10;
            my $strand="";
	    my @z=split(/M/, $f[5]);

            if (($f[5]=~/S$/)&&(($f[1] & 16) == 16))
            {
		my (@cigar_m)=$f[5]=~/(\d+)M/g;
                my (@cigar_d)=$f[5]=~/(\d+)D/g;
                my (@cigar_s)=$f[5]=~/(\d+)S/g;
                my (@cigar_i)=$f[5]=~/(\d+)I/g;

#		    print "$clipseq\t$rightseq\t$overcoor\t";
		    if ($overcoor > -1) {$overcoor += ($a[4] - 149);}
		}
#		print "\n";
            }
            elsif ((($f[1] & 32) == 32)&&($z[0]=~/S/)) {
		$coor=$f[3]; $strand="+";
		my (@clipped)=$z[0]=~/(\d+)S/g;
                my $cliplen=sum(@clipped);
#		print "$f[0]\n";
#		print "$cliplen\t";