bio::seqanalysisparseri(3pm) [debian man page]
Bio::SeqAnalysisParserI(3pm) User Contributed Perl Documentation Bio::SeqAnalysisParserI(3pm) 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, " "; } 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://redmine.open-bio.org/projects/bioperl/ 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 perl v5.14.2 2012-03-02 Bio::SeqAnalysisParserI(3pm)
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Bio::Factory::SeqAnalysisParserFactoryI(3pm) User Contributed Perl Documentation Bio::Factory::SeqAnalysisParserFactoryI(3pm) NAME
Bio::Factory::SeqAnalysisParserFactoryI - interface describing objects capable of creating SeqAnalysisParserI compliant parsers SYNOPSIS
# initialize an object implementing this interface, e.g. $factory = Bio::Factory::SeqAnalysisParserFactory->new(); # obtain a parser object $parser = $factory->get_parser(-input=>$inputobj, -params=>[@params], -method => $method); # $parser is an object implementing Bio::SeqAnalysisParserI # annotate sequence with features produced by parser while(my $feat = $parser->next_feature()) { $seq->add_SeqFeature($feat); } DESCRIPTION
This is an interface for factory classes capable of instantiating SeqAnalysisParserI implementing parsers. The concept behind the interface is a generic analysis result parsing in high-throughput automated sequence annotation pipelines. See Bio::SeqAnalysisParserI for more documentation of this concept. 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://redmine.open-bio.org/projects/bioperl/ 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 _ get_parser Title : get_parser Usage : $factory->get_parser(-input=>$inputobj, [ -params=>[@params] ], -method => $method) Function: Creates and returns a parser object for the given input and method. The type of input which is suitable depends on the implementation, but a good-style implementation should allow both file names and streams (filehandles). A particular implementation may not be able to create a parser for the requested method. In this case it shall return undef. Parameters (-params argument) are passed on to the parser object and therefore are specific to the parser to be created. An implementation of this interface should make this argument optional. Example : Returns : A Bio::SeqAnalysisParserI implementing object. Args : B<input> - object/file where analysis results are coming from, B<params> - parameter to use when parsing/running analysis B<method> - method of analysis perl v5.14.2 2012-03-02 Bio::Factory::SeqAnalysisParserFactoryI(3pm)