Re: Find overlap

[remiah]

Hello lunseyr.

I guess maybe something like this ...Input <DATA> may be diffrent from your files. This example prints

overlaps:9,200
no overlaps for chr2

I just thought packages may be good for adding constraints to your items.

Here I used Moose, but I am feeling something not good. I hope someone points me for better design.

use strict;
use warnings;

{ #packages to use
package Item;
use Any::Moose;
has "file" => (isa =>"Str", required=>1, is=>"rw");
has "bgn"  => (isa =>"Int", required=>1, is=>"rw");
has "end"  => (isa =>"Int", required=>1, is=>"rw");
1;

package overlaps;
use Any::Moose;
has "items" => (isa =>"ArrayRef[Item]", is=>"rw");
sub find_overlaps {
    my $self=shift;
    my $cur_bgn=undef;
    my $cur_end=undef;

    for (@{ $self->items }){
        #printf "%s,%d,%d\n", $_->file, $_->bgn,$_->end;
        if (! defined($cur_bgn) || ! defined($cur_end) ){
            $cur_bgn =$_->bgn;
            $cur_end =$_->end;
            next;
        }

        if ( ( $_->bgn >= $cur_bgn && $_->bgn <= $cur_end ) or
             ( $_->end >= $cur_bgn && $_->end <= $cur_end ) ){
            #ok
        }else {
            return undef;
        }

        $cur_bgn = $_->bgn if ( $_->bgn < $cur_bgn );
        $cur_end = $_->end if ( $_->end > $cur_end );
    }

    return [$cur_bgn, $cur_end];
}
1;
} #end packages to use

my %h;

#read data to hash
$/="";
while(<DATA>){
    my @rec=split /\n/;
    $rec[0] =~ s/^file:\s*//;
    my($k,$bgn,$end)=split /\s+/, $rec[1];
    push @{$h{$k}} , Item->new(file=>$rec[0],bgn=>$bgn,end=>$end);
}

#check overlaps
foreach my $k (keys %h){
    my $o=overlaps->new(items=>$h{$k});
    my $ret=$o->find_overlaps;
    if ($ret){
        print "overlaps:", join(',', @$ret) ,"\n";
    } else {
        print "no overlaps for $k\n";
    }
}

__DATA__
file: 148N
chr1    10    50

file: 162N
chr1    9       40

file: 174N
chr1    12      60

file: 175N
chr1    30      45

file: test
chr1    10     200

file: test2
chr2    1     3

file: test3
chr2    5     10

regards.