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