[Bioperl-l] Bio::Seq issue

Paolo Pavan paolo.pavan at gmail.com
Thu May 31 11:34:11 EDT 2012

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

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

Best regards,
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