[Bioperl-l] return type of $feature->seq() (comments on a commit [bioperl/bioperl-live fcd90e0])

Adam Sjøgren adsj at novozymes.com
Tue Jun 1 09:42:02 EDT 2010

Ok, so coming back to the reason for the changes in my fork¹.

It has been a while (the test in the application I am working on is from
August 2007, so I have been using/carrying the patch for three years²),
so I have to dig a little before it comes back to me.

Basically, I would like to make a class that inherits from
Bio::Seq::RichSeq and extends it. When I call ->seq on features on my
modules, I'd like to get an object of my own type back.

That sounds a little convoluted, so let me illustrate my thinking with a
self-contained script you can run:

= = =

use strict;
use warnings;

use Bio::SeqFeature::Generic;

my $seq=MySeq->new(-seq=>'actg');
print "len: " . length($seq->seq) . "\n";

my $new_feature=Bio::SeqFeature::Generic->new(-primary=>'source', -start=>2, -end=>3, -strand=>1);

foreach my $feature ($seq->get_SeqFeatures) {
    my $obj=$feature->seq;
    print ref($obj) . "len: " . length($obj->seq);
    print $obj->can('extra_method') ? " OK\n" : " FAIL\n";

exit 0;

package MySeq;

use base qw(Bio::Seq::RichSeq);

sub extra_accessor {
    # ...

sub extra_method {
    # ...
    print "extra_method called\n";

# ...

= = =

The output I expect (what my changes give rise to) is:

  extra_method called
  len: 4
  MySeqlen: 2 OK
  extra_method called

But the output I get is:

  extra_method called
  len: 4
  Bio::PrimarySeqlen: 2 FAIL
  Can't locate object method "extra_method" via package "Bio::PrimarySeq" at ./seq_inh_test.pl line 21.

That is what the changes on my fork try to address.

If there is a better way to accomplish the same result, I'd be flowing
over with joy :-)

  Best regards,


¹ http://github.com/adsj/bioperl-live - this commit in particular:
   - http://github.com/adsj/bioperl-live/commit/24ec961b217084e248f4fdbd174aadace1a27ac4

² There actually was a little discussion about this, way back, on this

   * Thread start, Oct 2006:
      - http://article.gmane.org/gmane.comp.lang.perl.bio.general/13224
   * Patch as per suggestions from Hilmar Lapp, Nov 2006:
      - http://article.gmane.org/gmane.comp.lang.perl.bio.general/13349

                                                          Adam Sjøgren
                                                    adsj at novozymes.com

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