[Bioperl-l] forcing alphabet in Bio::AlignIO
Mark A. Jensen
maj at fortinbras.us
Fri Jan 22 07:34:59 EST 2010
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 Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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