[Bioperl-l] SimpleAlign - get_seq_by_id

Jason Stajich jason at bioperl.org
Sat Oct 25 11:47:12 EDT 2008


you're right - it should be rolled back. I guess each_seq_xxx gets the  
job done.

We have a real problem with each vs get for our API mixture. I think  
there had been some logic there at one point but I think it is  
confusingly mixed now.
Perhaps a cleaned up API with deprecated aliases would be okay way to  
at some point move towards more standardized.

It would make sense to also see about implementing Gblocks style  
filtering method as well (but not in SimpleAlign give then number of  
methods already as you mention!).

-jason
On Oct 24, 2008, at 3:05 AM, Heikki Lehvaslaiho wrote:

> 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
> ___ _/_/_/_/_/________________________________________________________
>
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Jason Stajich
jason at bioperl.org





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