Bio::SeqAnalysisParserI - Sequence analysis output parser interface


    # get a SeqAnalysisParserI somehow, e.g. by
    my $parser = Bio::Factory::SeqAnalysisParserFactory->get_parser(
                            '-input' => 'inputfile', '-method' => 'genscan');
    while( my $feature = $parser->next_feature() ) {
        print "Feature from ", $feature->start, " to ", $feature->end, "\n";


SeqAnalysisParserI is a generic interface for describing sequence analysis result parsers. Sequence analysis in this sense is a search for similarities or the identification of features on the sequence, like a databank search or a a gene prediction result.

The concept behind this interface is to have a generic interface in sequence annotation pipelines (as used e.g. in high-throughput automated sequence annotation). This interface enables plug-and-play for new analysis methods and their corresponding parsers without the necessity for modifying the core of the annotation pipeline. In this concept the annotation pipeline has to rely on only a list of methods for which to process the results, and a factory from which it can obtain the corresponding parser implementing this interface.

See Bio::Factory::SeqAnalysisParserFactoryI and Bio::Factory::SeqAnalysisParserFactory for interface and an implementation of the corresponding factory.


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AUTHOR - Hilmar Lapp, Jason Stajich

Email Hilmar Lapp <>, Jason Stajich <>


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : next_feature
 Usage   : $seqfeature = $obj->next_feature();
 Function: Returns the next feature available in the analysis result, or
           undef if there are no more features.
 Example :
 Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
           more features.
 Args    : none