[Bioperl-l] forcing alphabet in Bio::AlignIO

Jason Stajich jason at bioperl.org
Fri Jan 22 14:18:30 EST 2010


Done, as of r16739. Look forward to the refactor work too.

-jason
On Jan 22, 2010, at 5:34 AM, Chris Fields wrote:

> Sounds good to me.  The warnings are a bit too tight on this module  
> anyway.
>
> I still think we have plans towards refactoring some of this, not  
> sure how far along they are:
>
> http://www.bioperl.org/wiki/Align_Refactor
>
> chris
>
> On Jan 22, 2010, at 12:17 AM, Jason Stajich wrote:
>
>> I'm considering putting in allowable initialization parameter (and  
>> get/set) for Bio::AlignIO that would allow setting of the  
>> alphabet.  This is then passed to Bio::LocatableSeq creation so  
>> that _guess_alphabet isn't called. This will allow removal of  
>> warnings about empty sequences because _guess_alphabet won't be  
>> called on a sequence if we have explictly set the alphabet.
>>
>> This worked great on my local install and tests pass.  Any  
>> objections or concerns?
>>
>> basically it means when you make an AlignIO you can specify the  
>> alphabet i.e.
>>
>> my $in = Bio::AlignIO->new(-format => 'fasta', -alphabet => 'dna', - 
>> file => 'genome.fasaln');
>>
>> I have some alignments with empty sequences and I think turning off  
>> the warnings is appropriate where I force the alphabet choice. It  
>> should also have a very modest speedup benefit too.
>>
>> -jason
>> --
>> Jason Stajich
>> jason.stajich at gmail.com
>> jason at bioperl.org
>> http://fungalgenomes.org/
>> http://twitter.com/hyphaltip
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/
http://twitter.com/hyphaltip



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