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

Jason Stajich jason at bioperl.org
Fri Jan 22 01:17:14 EST 2010

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 Stajich
jason.stajich at gmail.com
jason at bioperl.org

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