Ewan Birney

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 $result = $parser->next_result() ) {
              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://bio.perl.org/MailList.html    - About the mailing lists

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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Steve Chervitz, Jason Stajich, Hilmar Lapp

Email sac@bioperl.org

Authors of Bio::SeqAnalysisParserI on which this module is based: Email jason@chg.mc.duke.edu 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

result_factory

 Title   : result_factory
 Usage   : $res_fact = $obj->result_factory;     (get)
         : $obj->result_factory( $factory );      (set)
 Function: Sets/Gets a factory object to create result objects for this AnalysisParser.
 Returns : Bio::Factory::ResultFactoryI object 
 Args    : Bio::Factory::ResultFactoryI object (when setting)
 Comments: A AnalysisParserI implementation should provide a default result factory.
           obtainable by the  default_result_factory_class() method.

default_result_factory_class

 Title   : default_result_factory_class
 Usage   : $res_factory = $obj->default_result_factory_class()->new( @args )
 Function: Returns the name of the default class to be used for creating
           Bio::AnalysisResultI objects.
 Example :
 Returns : A string containing the name of a class that implements 
           the Bio::Factory::ResultFactoryI interface.
 Args    : none