NAME

Bio::SeqAnalysisParserI - Sequence analysis output parser interface

SYNOPSIS

    # 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";
    }

DESCRIPTION

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.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Hilmar Lapp, Jason Stajich

Email Hilmar Lapp <hlapp@gmx.net>, Jason Stajich <jason@bioperl.org>

APPENDIX

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

next_feature

 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