Bio::SeqFeature::ToolsUserHContributed PerBio::SeqFeature::Tools::IDHandler(3)NAMEBio::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
perl v5.14.12011-07-Bio::SeqFeature::Tools::IDHandler(3)
