comparison scripts/pickOverlapPair.ex.pl @ 21:9672fe07a232 draft default tip

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

20:6e02b9179a24

    my $rightlower=$right-500;
    my $rightupper=$right+500;
    my $chr_num=$a[0];
    $chr_num =~ s/chr//;
    if (($chrs{$a[0]} == 1) && (! defined $chrs{$chr_num})) {$chr_num=$a[0];}
    system("samtools view -Xf 0x2 $title $chr_num\:$leftlower\-$leftupper $chr_num\:$rightlower\-$rightupper > temp.sam");
    
    open in,"temp.sam";
    my %ps=();
    my %me=();
    my %uniqp=();

    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:(.)/;
	
	## Coordinate
	my $coor=$f[3];
	if ($f[1]=~/r/)
	{
	    if ($xt eq "U") {$uniqm{$f[0]}=1;}
	    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;
	    my $aln_ln=sum(@cigar_m,@cigar_d);
	    $me{$f[0]}=$f[3]+$aln_ln-1;
	}
	elsif ($f[1]=~/R/) {
	    $ps{$f[0]}=$f[3];
	    if ($xt eq "U") {$uniqp{$f[0]}=1;}
	}
	
#	${$pe{$f[0]}}[$rnum-1]=[$xt,$coor];

21:9672fe07a232

    my $rightlower=$right-500;
    my $rightupper=$right+500;
    my $chr_num=$a[0];
    $chr_num =~ s/chr//;
    if (($chrs{$a[0]} == 1) && (! defined $chrs{$chr_num})) {$chr_num=$a[0];}
    system("samtools view -f 0x2 $title $chr_num\:$leftlower\-$leftupper $chr_num\:$rightlower\-$rightupper > temp.sam");
    
    open in,"temp.sam";
    my %ps=();
    my %me=();
    my %uniqp=();

    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:(.)/;
	
	## Coordinate
	my $coor=$f[3];
	if (($f[1] & 16) == 16)
	{
	    if ($xt eq "U") {$uniqm{$f[0]}=1;}
	    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;
	    my $aln_ln=sum(@cigar_m,@cigar_d);
	    $me{$f[0]}=$f[3]+$aln_ln-1;
	}
	elsif (($f[1] & 32) == 32) {
	    $ps{$f[0]}=$f[3];
	    if ($xt eq "U") {$uniqp{$f[0]}=1;}
	}
	
#	${$pe{$f[0]}}[$rnum-1]=[$xt,$coor];