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Bio::AnalysisParserI(3User Contributed Perl DocumentatiBio::AnalysisParserI(3)

NAME
       Bio::AnalysisParserI - Generic analysis output parser interface

SYNOPSIS
	   # get a AnalysisParserI somehow.
	   # Eventually, there may be an Bio::Factory::AnalysisParserFactory.
	   # For now a SearchIO object, an implementation of AnalysisParserI, can be created
	   # directly, as in the following:
	   my $parser = Bio::SearchIO->new(
					   '-file'   => 'inputfile',
					   '-format' => 'blast');

	   while( my $result = $parser->next_result() ) {
	       print "Result:  ", $result->analysis_method,
		     ", Query:	", $result->query_name, "\n";

		 while( my $feature = $result->next_feature() ) {
		     print "Feature from ", $feature->start, " to ",
			   $feature->end, "\n";
		 }
	   }

DESCRIPTION
       AnalysisParserI is a interface for describing generic analysis result
       parsers. This module makes no assumption about the nature of analysis
       being parsed, only that zero or more result sets can be obtained from
       the input source.

       This module was derived from Bio::SeqAnalysisParserI, the differences
       being

       1. next_feature() was replaced with next_result().
	   Instead of flattening a stream containing potentially multiple
	   analysis results into a single set of features, AnalysisParserI
	   segments the stream in terms of analysis result sets
	   (Bio::AnalysisResultI objects). Each AnalysisResultI can then be
	   queried for its features (if any) as well as other information
	   about the result

       2. AnalysisParserI is a pure interface.
	   It does not inherit from Bio::Root::RootI and does not provide a
	   new() method. Implementations are free to choose how to implement
	   it.

   Rationale (copied from Bio::SeqAnalysisParserI)
       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.

   TODO
       Create Bio::Factory::AnalysisParserFactoryI and
       Bio::Factory::AnalysisParserFactory for interface and an
       implementation.	Note that this factory could return
       Bio::SearchIO-derived objects.

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:

	 http://bugzilla.open-bio.org/

AUTHOR - Steve Chervitz, Jason Stajich, Hilmar Lapp
       Email sac@bioperl.org

       Authors of Bio::SeqAnalysisParserI on which this module is based: Email
       jason@bioperl.org Email hlapp@gmx.net

COPYRIGHT
       Copyright (c) 2001 Steve Chervitz. All Rights Reserved.

DISCLAIMER
       This software is provided "as is" without warranty of any kind.

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

   next_result
	Title	: next_result
	Usage	: $result = $obj->next_result();
	Function: Returns the next result available from the input, or
		  undef if there are no more results.
	Example :
	Returns : A Bio::Search::Result::ResultI implementing object,
		  or undef if there are no more results.
	Args	: none

perl v5.14.1			  2011-07-22	       Bio::AnalysisParserI(3)
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