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

[Mark A. Jensen]

I'm down with that.

----- Original Message ----- 
From: "Jason Stajich" <jason at bioperl.org>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Friday, January 22, 2010 1:17 AM
Subject: [Bioperl-l] forcing alphabet in Bio::AlignIO


> 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
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