Bio::SeqFeature::Tools::FeatureNamer(3) generates unique persistent names for features


use Bio::SeqIO;
use Bio::SeqFeature::Tools::FeatureNamer;
# first fetch a genbank SeqI object
$seqio =
$seq = $seqio->next_seq();
$namer = Bio::SeqFeature::Tools::FeatureNamer->new;
my @features = $seq->get_SeqFeatures;
foreach my $feature (@features) {
$namer->name_feature($feature) unless $feature->display_name;


This is a helper class for providing names for SeqFeatures

The Bio::SeqFeatureI class provides a display_name method. Typically the display_name is not set when parsing formats such as genbank - instead properties such as label, product or gene are set in a somewhat inconsistent manner.

In addition, when generating subfeatures (for example, exons that are subfeatures of a transcript feature), it is often desirable to name these subfeatures before either exporting to another format or reporting to the user.

This module is intended to help given uniform display_names to features and their subfeatures.


Currently the naming policy is hardcoded. It may be desirable to allow plugging in variations on naming policies; this could be done either by subclassing, anonymous subroutines (closures) or parameterization. Contact the author if you feel you have need for a different naming policy


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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.

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AUTHOR - Chris Mungall

Email: cjm AT fruitfly DOT org


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : $unflattener = Bio::SeqFeature::Tools::FeatureNamer->new();
 Function: constructor
 Example : 
 Returns : a new Bio::SeqFeature::Tools::FeatureNamer
 Args    : see below


 Title   : name_feature
 Usage   : $namer->name_feature($sf);
 Function: sets display_name
 Example :
 Returns : 
 Args    : L<Bio::SeqFeatureI>

This method calls generate_feature_name() and uses the returned value to set the display_name of the feature


 Title   : name_contained_features
 Usage   : $namer->name_contained_features($sf);
 Function: sets display_name for all features contained by sf
 Example :
 Returns : 
 Args    : L<Bio::SeqFeatureI>

iterates through all subfeatures of a certain feature (using get_all_SeqFeatures) and names each subfeatures, based on the generated name for the holder feature

A subfeature is named by concatenating the generated name of the container feature with the type and a number.

For example, if the containing feature is a gene with display name dpp, subfeatures will be named dpp-mRNA-1 dpp-mRNA2 dpp-exon1 dpp-exon2 etc


 Title   : generate_feature_name
 Usage   : $name = $namer->generate_feature_name($sf);
 Function: derives a sensible human readable name for a $sf
 Example :
 Returns : str
 Args    : L<Bio::SeqFeatureI>

returns a generated name (but does not actually set display_name).

If display_name is already set, the method will return this

Otherwise, the name will depend on the property:


(in order of priority)