Bio::SeqFeature::TypedSeqFeatureI - a strongly typed SeqFeature
# get Sequence Features in some manner, eg # from a Sequence object foreach $sf ( $seq->get_SeqFeatures() ) { # all sequence features must have primary_tag() return a string $type_as_string = $sf->primary_tag(); if( $sf->isa("Bio::SeqFeature::TypedSeqFeatureI") ) { $ot = $sf->ontology_term(); print "Ontology identifier:",$ot->identifier(), " name:",$ot->name(), " Description:",$ot->description(),"\n"; } else { print "Sequence Feature does not have an ontology type\n"; } }
This interface describes the extension of SeqFeatureI to being a strongly typed SeqFeature.
Bio::SeqFeature::TypedSeqFeatureI extends the Bio::SeqFeatureI interface (ie, a TypedSeqFeatureI feature must also implement all the Bio::SeqFeatureI interface as well).
It is suggested that the primary_tag() method of SeqFeatureI return the same as the ontology_term()->name() of the OntologyTypedI (ie, the "string" name of the ontology type is used as the primary tag), but this should not be assummed by client code as they are scenarios where one would like to maintain the difference.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : ontology_term Usage : my $ot = $seqfeature->ontology_term() Returns : a Bio::Ontology::TermI compliant object Args : none Status : public
This method returns the ontology term for a strongly typed sequence feature.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.