[Bioperl-l] new interfaces, classes
Wed, 6 Sep 2000 14:45:41 -0400 (EDT)
Hilmar and I have been trying to put together a simple method for adding
features to sequences from a variety of sources. To faciltitate this 2
new interfaces are proposed (and have been submitted to CVS) [excusing
the pseudo-perl function definitions below].
Bio::SeqAnalysisParserI - provides the routines for parsing SeqAnalysis
output. This can be from a file, filestream,
Bio::SeqFeatureProducerI - provides an interface for adding features to a
Additionally, one module has been written that implements
Bio::SeqFeatureProducer - implements Bio::SeqFeatureProducerI and consumes
features from the parser object until next_feature is exhausted.
Each retrieved feature is populated on the sequence object.
* Bio::SeqAnalysisParser - a driver class in the SeqIO spirit which will
allow a user to do the following (we are instantiating a parser on the
parse command rather than in new).
my $parser = new Bio::SeqAnalysisParser();
$parser->parse(-input=>'filename', -method=>'MZEF',-params [ (
my $featprod = new Bio::SeqFeatureProducer();
* Connect the Bio::Tools::Sim4, Bio::Tools::BPlite, Bio::Tools::HMMER
parsers into this system.
Comments, criticism, and volunteers welcome.
Center for Human Genetics - Duke University Medical Center