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

Cook, Malcolm MEC at stowers-institute.org
Wed May 3 11:09:04 EDT 2006


Marco,

It appears that your code assumes that the exons as returned from call
to BIO::DB::GFF::features are sorted by start; I don't think is
guaranteed (at least not in the documentation I'm reading).  Also I
think your code will not report overlap between two exons that have an
intervening overlapping exon.  Depending on what you're application is,
you may care.  For example, e1, e2, e3 all intersect pairwise, but your
code won't report on e1's overlap with e3.

e1 ---*******-------
e2 -----******------
e3 ------***--------

Out of curiousity, what is your application?  Designing primers for gene
resequencing?

Cheers,

Malcolm Cook
Database Applications Manager, Bioinformatics
Stowers Institute for Medical Research 

>-----Original Message-----
>From: bioperl-l-bounces at lists.open-bio.org 
>[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
>Marco Blanchette
>Sent: Tuesday, May 02, 2006 2:31 PM
>To: bioperl-l at lists.open-bio.org
>Subject: [Bioperl-l] Bio::RangeI intersection and Bio::DB::GFF
>
>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
>-- 
>
>
>
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