[Bioperl-l] forcing alphabet in Bio::AlignIO
Jason Stajich
jason at bioperl.org
Fri Jan 22 06:17:14 UTC 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
--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/
http://twitter.com/hyphaltip
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