[Bioperl-l] informative codons method for kaks --Bio/Align/DNAStatistics.pm

Albert Vilella avilella at gmail.com
Fri Aug 18 07:02:57 EDT 2006


Upon closer inspection, it turned out to be a one-liner!

=head2 kaks_pattern_number

 Title   : kaks_pattern_number
 Usage   : my $patterns = $stats->kaks_pattern_number($alnobj);
 Function: Counts the number of codons with no gaps in the MSA
 Returns : Number of codons with no gaps ('patterns' in PAML notation)
 Args    : A Bio::Align::AlignI compliant object such as a
            Bio::SimpleAlign object.

=cut

sub kaks_pattern_number{
    my ($self, $aln) = @_;
    return ($aln->remove_gaps->length)/3;
}

How do you like the method name? Suggestions?

    Albert.

On Thu, 2006-08-17 at 11:39 -0500, Chris Fields wrote:
> Albert,
> 
> Might be a good idea to start working on those!  Nice to use Bugzilla as a
> repository for ideas, but we're heading towards using the Bioperl wiki for
> that more now.
> 
> Chris
> 
> > -----Original Message-----
> > From: Albert Vilella [mailto:avilella at gmail.com]
> > Sent: Thursday, August 17, 2006 11:17 AM
> > To: Chris Fields
> > Cc: bioperl-l at bioperl.org
> > Subject: Re: [Bioperl-l] informative codons method for kaks --
> > Bio/Align/DNAStatistics.pm
> > 
> > I will opt for the "return the number of informative codons" then, which
> > is the easiest :)
> > 
> > I don't know when is this going to be there if it depends on me,
> > though... my list of 'enh' bug tickets is growing shamefully fast :p
> > 
> > Cheers,
> > 
> >     Albert.
> > 
> > On Thu, 2006-08-17 at 09:26 -0500, Chris Fields wrote:
> > > Sure, why not?  If you (or someone) can add one in, I don't see how
> > > it could hurt.
> > >
> > > Make sure to add tests for this in the proper test suite.
> > >
> > > Chris
> > >
> > > On Aug 17, 2006, at 6:37 AM, Albert Vilella wrote:
> > >
> > > > Hi all,
> > > >
> > > > I think it would be nice to have a method in
> > > > Bio/Align/DNAStatistics.pm that gives the number of informative codons
> > > > for kaks in a MSA. That is, the codons that are used in the
> > > > calculation of kaks. This, AFAICS, more or less what codeml calls
> > > > "patterns".
> > > >
> > > > I often find myself in the situation of wanting to know how big is the
> > > > CDS alignment not in terms of sequence length, but of the number of
> > > > codons that are going to be used in the kaks statistics. I guess this
> > > > method would help in that.
> > > >
> > > > The method could:
> > > >
> > > > return the number of informative codons?
> > > > maybe return a new seqarray with only the informative codons?
> > > >
> > > > What do you think? Jason? Chris?
> > > >
> > > > http://bugzilla.open-bio.org/show_bug.cgi?id=2078
> > > >
> > > > Bests,
> > > >
> > > >     Albert.
> > > >
> > > >
> > > > _______________________________________________
> > > > Bioperl-l mailing list
> > > > Bioperl-l at lists.open-bio.org
> > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > >
> > > Christopher Fields
> > > Postdoctoral Researcher
> > > Lab of Dr. Robert Switzer
> > > Dept of Biochemistry
> > > University of Illinois Urbana-Champaign
> > >
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



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