[Bioperl-l] SimpleAlign - get_seq_by_id

Rutger Vos rvos at interchange.ubc.ca
Fri Oct 24 02:40:25 EDT 2008


I would be very hesitant to introduce array contexts - it just yields
subtle bugs and maintenance issues. Perhaps a separate
get_all_seqs_by_id would be better?

On Fri, Oct 24, 2008 at 2:32 PM, Heikki Lehvaslaiho <heikki at sanbi.ac.za> 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
>>
>>
>>
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>
> --
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>  _/  _/  _/  University of Western Cape, South Africa
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-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com


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