Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
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:

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

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 v5.32.1			  2019-12-07	       Bio::AnalysisParserI(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Steve Chervitz, Jason Stajich, Hilmar Lapp | COPYRIGHT | DISCLAIMER | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::AnalysisParserI&sektion=3&manpath=FreeBSD+13.0-RELEASE+and+Ports>

home | help