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Bio::SeqFeature::Tools::IDHandler.3pm

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:

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

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 seperate entity