[Bioperl-l] Re: DNA topology

[Heikki Lehvaslaiho]

Yes, of course. I fixed that myself at some point. My memory is going,
going.. Now, what were we talking about?

	-Heikki

On Fri, 2002-11-15 at 15:33, Jason Stajich wrote:
> I think it's easier than that.  Don't we have a function
> 
> $seq->is_circular
> 
> Which will get set to true if it is circular?
> 
> >From Bio/SeqIO/genbank.pm:
>        my $circ = shift(@tokens);
>           if ($circ eq 'circular') {
>               $params{'-is_circular'} = 1;
>               $params{'-division'} = shift(@tokens);
>           } else {
>               # 'linear' or 'circular' may actually be omitted altogether
>               $params{'-division'} =
>                   (CORE::length($circ) == 3 ) ? $circ : shift(@tokens);
>           }
> 
> -jason
> On 15 Nov 2002, Heikki Lehvaslaiho wrote:
> 
> > Jing,
> >
> > RefSeq loosely follows GenBank format. In GenBank, the LOCUS line can
> > contain the word 'circular'. That word should be part of the string
> > returned by the Bio::Seq::RichSeq::division method. I am not sure if
> > there are any circular molecules in RefSeq.
> >
> > Try:
> >
> > if ($seq->division =~ /circular/ ) {
> >
> > } else { #linear
> >
> > }
> >
> >
> > Yours,
> > 	-Heikki
> >
> >
> > On Fri, 2002-11-15 at 13:56, jzhao wrote:
> > > Mr. Lehvaslaiho,
> > >
> > > I am wrapping some BioPerl modules to retrieve genome features from the
> > > RefSeq database. Is there any handy methods that can tell whether the DNA
> > > is linear or circular?
> > >
> > > Thanks,
> > > Jing
> > >
> >
-- 
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     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
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