Bio::SeqFeature::Tools::FeatureNamer(3pm) User Contributed Perl Documentation Bio::SeqFeature::Tools::FeatureNamer(3pm)
NAME
Bio::SeqFeature::Tools::FeatureNamer - generates unique persistent names for features
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.
TODO
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
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 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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chris Mungall
Email: cjm AT fruitfly DOT org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : $unflattener = Bio::SeqFeature::Tools::FeatureNamer->new();
Function: constructor
Example :
Returns : a new Bio::SeqFeature::Tools::FeatureNamer
Args : see below
name_feature
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
name_contained_features
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
generate_feature_name
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:
label
product
gene
locus_tag
(in order of priority)
perl v5.14.2 2012-03-02 Bio::SeqFeature::Tools::FeatureNamer(3pm)