Bio::SeqFeature::Tools FeatureNamer
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Summary
Bio::SeqFeature::Tools::FeatureNamer - generates unique persistent names for features
Package variables
No package variables defined.
Inherit
Bio::Root::Root
Synopsis
  use Bio::SeqIO;
use Bio::SeqFeature::Tools::FeatureNamer;
# first fetch a genbank SeqI object $seqio = Bio::SeqIO->new(-file=>'AE003644.gbk', -format=>'GenBank'); $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; }
Description
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.
Methods
newDescriptionCode
name_featureDescriptionCode
name_contained_featuresDescriptionCode
generate_feature_nameDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : $unflattener = Bio::SeqFeature::Tools::FeatureNamer->new();
Function: constructor
Example :
Returns : a new Bio::SeqFeature::Tools::FeatureNamer
Args : see below
name_featurecodeprevnextTop
 Title   : name_feature
Usage : $namer->name_feature($sf);
Function: sets display_name
Example :
Returns :
Args : Bio::SeqFeatureI
This method calls generate_feature_name() and uses the returned value
to set the display_name of the feature
name_contained_featurescodeprevnextTop
 Title   : name_contained_features
Usage : $namer->name_contained_features($sf);
Function: sets display_name for all features contained by sf
Example :
Returns :
Args : 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
generate_feature_namecodeprevnextTop
 Title   : generate_feature_name
Usage : $name = $namer->generate_feature_name($sf);
Function: derives a sensible human readable name for a $sf
Example :
Returns : str
Args : Bio::SeqFeatureI
returns a generated name (but does not actually set display_name).
If display_name is already set, the method will return this
Otherwise, the name will depend on the property:
    label
    product
    gene
    locus_tag
(in order of priority)
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);

#    my($typemap) =
# $self->_rearrange([qw(TYPEMAP
# )],
# @args);#
# $typemap && $self->typemap($typemap);
return $self; # success - we hope!
}
name_featuredescriptionprevnextTop
sub name_feature {
    my ($self, $sf) = @_;
    my $name = $self->generate_feature_name($sf);
    $sf->display_name($name);
}
name_contained_featuresdescriptionprevnextTop
sub name_contained_features {
   my ($self,$sf) = @_;
   my $cname = $self->generate_feature_name($sf);
   my @subsfs = $sf->get_all_SeqFeatures;
   my %num_by_type = ();
   foreach my $ssf (@subsfs) {
       my $type = $ssf->primary_tag;
       my $num = $num_by_type{$type} || 0;
       $num++;
       $num_by_type{$type} = $num;
       $ssf->display_name("$cname-$type-$num");
   }
   return;
}
generate_feature_namedescriptionprevnextTop
sub generate_feature_name {
    my ($self, $sf) = @_;

    my $name = $sf->display_name;
    if (!$name) {
	if ($sf->has_tag("label")) {
	    ($name) = $sf->get_tag_values("label");
	}
	elsif ($sf->has_tag("product")) {
	    ($name) = $sf->get_tag_values("product");
	}
	elsif ($sf->primary_tag eq 'gene' &&
	       $sf->has_tag("gene")) {
	    ($name) = $sf->get_tag_values("gene");
	}
	elsif ($sf->primary_tag eq 'gene' &&
	       $sf->has_tag("locus_tag")) {
	    ($name) = $sf->get_tag_values("locus_tag");
	}
	else {
	    $name =  $sf->display_name;
	}
    }
    return $name;
}

1;
}
General documentation
TODOTop
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
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to 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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chris MungallTop
Email: cjm AT fruitfly DOT org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _