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)

Bio::Tools::ESTScan(3pm)				User Contributed Perl Documentation				  Bio::Tools::ESTScan(3pm)

NAME

       Bio::Tools::ESTScan - Results of one ESTScan run

SYNOPSIS

	  $estscan = Bio::Tools::ESTScan->new(-file => 'result.estscan');
	  # filehandle:
	  $estscan = Bio::Tools::ESTScan->new( -fh  => *INPUT );

	  # parse the results
	  # note: this class is-a Bio::Tools::AnalysisResult which implements
	  # Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same
	  while($gene = $estscan->next_prediction()) {
	      # $gene is an instance of Bio::Tools::Prediction::Gene
	      foreach my $orf ($gene->exons()) {
		  # $orf is an instance of Bio::Tools::Prediction::Exon
		  $cds_str = $orf->predicted_cds();
	      }
	  }

	  # essential if you gave a filename at initialization (otherwise the file
	  # will stay open)
	  $estscan->close();

DESCRIPTION

       The ESTScan module provides a parser for ESTScan coding region prediction output.

       This module inherits off Bio::Tools::AnalysisResult and therefore implements the Bio::SeqAnalysisParserI interface.  See
       Bio::SeqAnalysisParserI.

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
       Email hlapp@gmx.net (or hilmar.lapp@pharma.novartis.com)

APPENDIX

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

   analysis_method
	Usage	  : $estscan->analysis_method();
	Purpose   : Inherited method. Overridden to ensure that the name matches
		    /estscan/i.
	Returns   : String
	Argument  : n/a

   next_feature
	Title	: next_feature
	Usage	: while($orf = $estscan->next_feature()) {
			 # do something
		  }
	Function: Returns the next gene structure prediction of the ESTScan result
		  file. Call this method repeatedly until FALSE is returned.

		  The returned object is actually a SeqFeatureI implementing object.
		  This method is required for classes implementing the
		  SeqAnalysisParserI interface, and is merely an alias for
		  next_prediction() at present.

	Example :
	Returns : A Bio::Tools::Prediction::Gene object.
	Args	:

   next_prediction
	Title	: next_prediction
	Usage	: while($gene = $estscan->next_prediction()) {
			 # do something
		  }
	Function: Returns the next gene structure prediction of the ESTScan result
		  file. Call this method repeatedly until FALSE is returned.

		  So far, this method DOES NOT work for reverse strand predictions,
		  even though the code looks like.
	Example :
	Returns : A Bio::Tools::Prediction::Gene object.
	Args	:

   close
	Title	: close
	Usage	: $result->close()
	Function: Closes the file handle associated with this result file.
		  Inherited method, overridden.
	Example :
	Returns :
	Args	:

   _fasta_stream
	Title	: _fasta_stream
	Usage	: $result->_fasta_stream()
	Function: Gets/Sets the FASTA sequence IO stream for reading the contents of
		  the file associated with this MZEF result object.

		  If called for the first time, creates the stream from the filehandle
		  if necessary.
	Example :
	Returns :
	Args	:

perl v5.14.2							    2012-03-02						  Bio::Tools::ESTScan(3pm)