[Bioperl-l] SimpleAlign - get_seq_by_id

Heikki Lehvaslaiho heikki at sanbi.ac.za
Fri Oct 24 02:32:49 EDT 2008


The main reason it has not been Bio::SeqAlign is that sequence ID not 
necessarily a unique identifier in a MSA. Multiple regions of the sequence 
defined by one ID can be in one.

The current code returns only the more or less randomly selected first 
Bio::LocatebleSeqI object with that ID. Should we make it context sensitive 
and return an array of sequences in array context? 

That brings up an other question: After the change, the get_seq_by_id() will 
behave differently from all other instances of that method, so should it be 
renamed to reflect that?

      -Heikkki

On Thursday 23 October 2008 21:29:20 Jason Stajich wrote:
> I added get_seq_by_id to Bio::SimpleAlign to allow retrieval of a
> particular sequence from the alignment by ID. Not sure why this didn't
> exist before.
>
> -jason
> --
> Jason Stajich
> jason at bioperl.org
>
>
>
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-- 
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     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
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