[Bioperl-l] planning sequence mutating modules

Heikki Lehvaslaiho heikki at sanbi.ac.za
Tue Feb 14 01:59:29 EST 2006


I've committed an interim solution to the sequence evolution problem:

    $newseq = Bio::SeqUtils-> evolve
        ($seq, $similarity, $transition_transversion_rate);

I will go on to transform this code to fully OO, extensible solution.

   -Heikki


On Friday 10 February 2006 09:06, Heikki Lehvaslaiho wrote:
> Ryan Golhar's mail got me thinking that we should have a simple framework
> for mutating sequences to a desired level. The model can then be extended
> to necessary complexity when needed by subclassing.
>
> To start with, I have been planning:
>
>
> Bio::SeqEvolution::EvolutionI - interface file
> Bio::SeqEvolution::EvolutionI::seq() - seq to mutate
> Bio::SeqEvolution::EvolutionI::seq_type() - returned seq class,
>         (defaults to Bio::PrimarySeq)
> Bio::SeqEvolution::EvolutionI::next_seq() - overridable by subclasses
> Bio::SeqEvolution::EvolutionI::each_seqs($count)
>        - returns an array of $count seqs
> Bio::SeqEvolution::EvolutionI::_generate_seq()
> Bio::SeqEvolution::EvolutionI::matrix  # Bio::Matrix::Scoring
>       converteed to probabilites of change internally
>
>   various methods to define the extent of divergence:
>   only one to start with:
> Bio::SeqEvolution::EvolutionI::pam() -percentage accepted mutation
>    (= 100% - identity)
>
> Bio::SeqEvolution::Factory - core class to call,
>          instantiates subclasses, Bio::SeqEvolution::DNASimple for
> nucleotides Bio::SeqEvolution::EvolutionI::type() - evolution model,
>       defaults to Bio::SeqEvolution::DNASimple for nucleotides
>
>
> Bio::SeqEvolution::DNASimple - default for nucleotides
> Bio::SeqEvolution::DNASimple::transversion_rate - positive integer,
>         e.g. 5 => 5:1, defaults to 1:1
>         simple alternative to a scoring matrix
>
>
> I am soliciting usual comments and suggestions about naming and minimal
> functionality.
>
>
>    -Heikki

-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________


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