[Bioperl-l] SimpleAlign - get_seq_by_id

Heikki Lehvaslaiho heikki at sanbi.ac.za
Fri Oct 24 03:05:27 EDT 2008


Spoke too soon: each_seq_with_id() already exists. Is there really a need for 
get_seq_by_id()?

A more general observation: Bio::SimpleAlign with its 83 methods has grown too 
big to keep all the code (3055 lines total) in one file. Any volunteers to 
break it up into more manageable chunks? 

The methods in the current file have already been categorised which should help 
in the task:

=head1 Modifier methods
=head1 Sequence selection methods
=head1 Create new alignments
=head1 Change sequences within the MSA
=head1 MSA attributes
=head1 Alignment descriptors
=head1 Alignment positions
=head1 Sequence names

The helper modules should go into Bio::Align name space.


   -Heikki


On Friday 24 October 2008 08:32:49 Heikki Lehvaslaiho wrote:
> 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
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Senior Scientist    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
___ _/_/_/_/_/________________________________________________________



More information about the Bioperl-l mailing list