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

Chris Fields cjfields at illinois.edu
Fri Jan 22 08:34:07 EST 2010


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
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> jason at bioperl.org
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