[Bioperl-l] Bio::RangeI intersection and Bio::DB::GFF

[Brian Osborne]

Marco,

Yes, this is how intersection() is supposed to work. If both of the Range
objects have the same strand then the strand information is returned as part
of the result but if they aren't on the same strand then no strand
information is returned.

Brian O.


On 5/2/06 3:30 PM, "Marco Blanchette" <mblanche at berkeley.edu> wrote:

> Dear all--
> 
> I have been trying to use the intersection function to extract overlapping
> region from alternatively spliced exons as in the following script. The
> returned object from the 'my $overlap = $exon1->intersection($exon2);' is
> actually loosing the strand of $exon1 if $exon1 is from the negative strand.
> Is this behavior expected? Should I check the strand of $exon1 before
> working on the object return by any Bio::RangeI function?
> 
> Many thanks 
> 
> #!/usr/bin/perl
> use strict;
> use warnings;
> use Bio::DB::GFF;
> 
> MAIN:{
> 
>     my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql',
>                                 -dsn =>
> 'dbi:mysql:database=dmel_43_LS;host=riolab.net',
>                                 -user => 'guest');
>     my $test_db = $db->segment('4');
>     
>     # Load up the exons into $exons_p
>     for my $gene ($test_db->features(-types => 'gene')){
> 
>         my $exons_p = extractExons($gene);
> 
>         cluster($exons_p) unless ($#{$exons_p} == -1);
> 
>     }
> }
> 
> sub extractExons {
>     my $gene = shift;
>     my %ex_list;
>     my @tcs = $gene->features(    -type =>'processed_transcript',
>                                     -attributes =>{Gene => $gene->group});
>                  
>     for my $tc (@tcs){
>         my @exons = $tc->features (-type => 'exon',
>                                      -attributes => {Parent => $tc->group}
> );        
>     
>         for (@exons){
>             my $ex_id    = $_->id;
>             $ex_list{$ex_id} = $_ unless (exists $ex_list{$ex_id});
> 
>         }
>     
>     }
>     my @values = values %ex_list;
>     return(\@values);
> }
> 
> sub cluster {
>     my $exons_p = shift;
>     
>     for (my $s = 0; $s <= $#{$exons_p}; $s++){
>         for (my $t = $s+1; $t <= $#{$exons_p}; $t++){
>             my $exon1 = $exons_p->[$s];
>             my $exon2 = $exons_p->[$t];
>             
>             if (!($exon1->equals($exon2)) && $exon1->overlaps($exon2)){
>             
>                 my $overlap = $exon1->intersection($exon2);
>                 
>                 print "===\n";;
>                 print "ex1\n", $exon1->seq, "\n";
>                 print "ex2\n", $exon2->seq, "\n";
>                 print "overlap\n", $overlap->seq, "\n";
>             }
>         }
>     }
> }
> ______________________________
> Marco Blanchette, Ph.D.
> 
> mblanche at uclink.berkeley.edu
> 
> Donald C. Rio's lab
> Department of Molecular and Cell Biology
> 16 Barker Hall
> University of California
> Berkeley, CA 94720-3204
> 
> Tel: (510) 642-1084
> Cell: (510) 847-0996
> Fax: (510) 642-6062