[Bioperl-l] Fwd: Bio::Seq issue

Paolo Pavan paolo.pavan at gmail.com
Thu Jun 7 04:09:42 EDT 2012


Hello,
I have the feeling that the email below was blocked by the mailer daemon
because "has a suspicious header", I believe most because has a "patch"
file attached so forgive me as I am sending it again.
If someone is interested to the file, I can send it not throught the
mailing list.

Regards,
Paolo


---------- Forwarded message ----------
From: Paolo Pavan <paolo.pavan at gmail.com>
Date: 2012/5/31
Subject: Bio::Seq issue
To: bioperl-l at lists.open-bio.org



Hello everyone again,
By the way, I think I have encountered a minor issue in the method
Bio::Seq->is_circular(), that is defined in the file Bio/Seq.pm as a pure
getter as:

sub is_circular { shift->primary_seq->is_circular }

while it's counterpart in Bio/PrimarySeq.pm is defined as a getter/setter
as:

sub is_circular{
    my $self = shift;
    return $self->{'is_circular'} = shift if @_;
    return $self->{'is_circular'};
}

the result is that if you have a Bio::Seq object, for instance read by
Bio::SeqIO you can't change any more the property (well, unless you do
$seq->primary_seq->is_circular($is_circular) ).

Do someone agree that they should have the same behaviour?
It the case, attached patch file applied to Bio/Seq.pm file should do the
job.

Best regards,
Paolo


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