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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:

   http://bugzilla.open-bio.org/
 
 

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)