Bio::SeqAnalysisParserUser Contributed Perl DocumentBio::SeqAnalysisParserI(3)NAMEBio::SeqAnalysisParserI - Sequence analysis output parser interface
SYNOPSIS
# get a SeqAnalysisParserI somehow, e.g. by
my $parser = Bio::Factory::SeqAnalysisParserFactory->get_parser(
'-input' => 'inputfile', '-method' => 'genscan');
while( my $feature = $parser->next_feature() ) {
print "Feature from ", $feature->start, " to ", $feature->end, "\n";
}
DESCRIPTION
SeqAnalysisParserI is a generic interface for describing sequence
analysis result parsers. Sequence analysis in this sense is a search
for similarities or the identification of features on the sequence,
like a databank search or a a gene prediction result.
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.
See Bio::Factory::SeqAnalysisParserFactoryI and
Bio::Factory::SeqAnalysisParserFactory for interface and an
implementation of the corresponding factory.
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 - Hilmar Lapp, Jason Stajich
Email Hilmar Lapp <hlapp@gmx.net>, Jason Stajich <jason@bioperl.org>
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
next_feature
Title : next_feature
Usage : $seqfeature = $obj->next_feature();
Function: Returns the next feature available in the analysis result, or
undef if there are no more features.
Example :
Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
more features.
Args : none
perl v5.14.1 2011-07-22 Bio::SeqAnalysisParserI(3)
