NAME

Bio::SeqFeature::Tools::IDHandler - maps $seq_feature->primary_tag

SYNOPSIS

  use Bio::SeqIO;
  use Bio::SeqFeature::Tools::IDHandler;

DESCRIPTION

Class to map $seq_feature->primary_tag

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Chris Mungall

Email: cjm@fruitfly.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::IDHandler->new();
 Function: constructor
 Example : 
 Returns : a new Bio::SeqFeature::Tools::IDHandler
 Args    : see below

set_ParentIDs_from_hierarchy()

 Title   : set_ParentIDs_from_hierarchy()
 Usage   : $idhandler->set_ParentIDs_from_hierarchy($fholder)
 Function: populates tags Parent and ID via holder hierarchy
 Example :
 Returns : 
 Args    : Bio::featureHolderI (either a SeqFeature or a Seq)

This is mainly for GFF3 export

GFF3 uses the tags ID and Parent to represent the feature containment hierarchy; it does NOT use the feature holder tree

This method sets Parent (and ID for any parents not set) based on feature holder/containement hierarchy, ready for GFF3 output

create_hierarchy_from_ParentIDs

 Title   : create_hierarchy_from_ParentIDs
 Usage   : $idhandler->set_ParentIDs_from_hierarchy($fholder)
 Function: inverse of set_ParentIDs_from_hierarchy
 Example :
 Returns : list of top SeqFeatures
 Args    :

generate_unique_persistent_id

 Title   : generate_unique_persistent_id
 Usage   :
 Function: generates a unique and persistent identifier for this
 Example :
 Returns : value of primary_id (a scalar)
 Args    :

Will generate an ID, and set primary_id() (see above)

The ID is a string generated from

  seq_id
  primary_tag
  start
  end

There are three underlying assumptions: that all the above accessors are set; that seq_id is a persistent and unique identifier for the sequence containing this feature; and that

  (seq_id, primary_tag, start, end)

is a "unique constraint" over features

The ID is persistent, so long as none of these values change - if they do, it is considered a separate entity