NAME¶
Bio::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:
https://github.com/bioperl/bioperl-live/issues
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