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