[Bioperl-l] Codon Table

[michael watson (IAH-C)]

Thanks Heidi, your efforts are appreciated :-)

-----Original Message-----
From: Heikki Lehvaslaiho [mailto:heikki at nildram.co.uk]
Sent: 25 October 2003 15:44
To: michael watson (IAH-C)
Cc: 'bioperl-l at bioperl.org'
Subject: Re: [Bioperl-l] Codon Table


Mick,

The PrimarySeq::translate interface is a mess, so adding one more
attribute the the end of the long list is not going to make much a
difference. I added the code into CVS.

	-Heikki


On Fri, 2003-10-17 at 14:51, Heikki Lehvaslaiho wrote:
> Mick,
> 
> I really have not thought about this possibility. CodonTable can easily
> be modified, but there is no way of passing the modified codontable
> object to sequence::translate. The translate function has really complex
> argument list already, so there is no way we can add anything in there. 
> 
> Depending what you want to do, it might be enough to modify the
> codontable object and use its translate function. Compare it to
> Bio::PrimarySeqI::translate to see what I mean. If you need full
> seq::translate functionality, Bio::SeqUtils is the place to put the
> code, e.g. $polypept = Bio::SeqUtils::translate($seq, $codontable);
> 
> I wrote the following method to be added into Bio::Tools::CodonTable. If
> you think it is useful, I can commit it.
> 
> Yours,
> 	-Heikki
> 
> 
> =head2 add_table
> 
>  Title   : add_table
>  Usage   : $newid = $ct->add_table($name, $table, $starts)
>  Function: Add a custom Codon Table into the object.
>            Know what you are doing, only the length of
>            the argument strings is checked!
>  Returns : the id of the new codon table
>  Args    : name, a string, optional (can be empty)
>            table, a string of 64 characters
>            startcodons, a string of 64 characters, defaults to standard
> 
> =cut
> 
> sub add_table {
>     my ($self, $name, $table, $starts) = @_;
> 
>     $name ||= 'Custom'. scalar @NAMES + 1;
>     $starts ||= $STARTS[0]; 
>     $self->throw('Suspect input!')
>         unless length($table) == 64 and length($starts) == 64;
> 
>     push @NAMES, $name;
>     push @TABLES, $table;
>     push @STARTS, $starts;
> 
>     return scalar @NAMES;
> 
> }
> 
> usage:
> 
> $ct_id = $ct->add_table(@custom_table);
> $ct->id($ct_id);
> $string = $ct->translate($nt_string);
> 
> 
>  
> 
> 
> 
> On Tue, 2003-10-14 at 17:03, michael watson (IAH-C) wrote:
> > Hi
> > 
> > I want to use a different codon table than any that are present in CodonTable.pm.  Does Bioperl have a way to implement this?  Or will I have to hack CodonTable.pm?
> > 
> > Thanks
> > Mick
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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