[Bioperl-l] three letter codes for amino acids?

[Ewan Birney]

On Wed, 10 Jan 2001, Heikki Lehvaslaiho wrote:

> 
> 
> I noticed that it is not possible to use three letter codes for amino
> acids in any bioperl sequence objects. I think should be possible at
> least to output in three letter code. Mapping three letter code back
> to one letter code is not too hard, either, but is it a good idea to
> have?
> 
> I propose to put method 'seq3' into PrimarySeq.pm which is called from
> Seq.pm, too.
> 
> =head2 seq3
> 
>  Title   : seq3
>  Usage   : $string = $obj->seq3()
>  Function: Read only method that returns the amino acid sequence 
>            as a string of three letter codes. moltype has to be 
>            'protein'. Output follows the IUPAC standard plus 
>            'Ter' for terminator.
>  Returns : A scalar
>  Args    : character used for stop, optional, defaults to '*'
>            character used for unknown, optional, defaults to 'X'
> 
> =cut
> 
> Any opinions?


Do you really want this? I guess so.


There could be an argument to make a SeqUtils class and move this sort of
function in there, allowing us to mess less objects/interfaces it would be


   $seq3 = Bio::SeqUtils->seq3($seq);


> 
> 	-Heikki
> 
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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