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