Bio SeqAnalysisParserI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::SeqAnalysisParserI - Sequence analysis output parser interface
Package variables
No package variables defined.
Included modules
    # 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";
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
See Bio::Factory::SeqAnalysisParserFactoryI and
Bio::Factory::SeqAnalysisParserFactory for interface and an implementation
of the corresponding factory.
Methods description
next_featurecode    nextTop
 Title   : next_feature
Usage : $seqfeature = $obj->next_feature();
Function: Returns the next feature available in the analysis result, or
undef if there are no more features.
Example :
Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
more features.
Args : none
Methods code
sub next_feature {
    my ($self) = shift;

General documentation
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Reporting BugsTop
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AUTHOR - Hilmar Lapp, Jason StajichTop
Email Hilmar Lapp <>, Jason Stajich <>
The rest of the documentation details each of the object methods.
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