Bio::SeqIO::game::featHandler.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::SeqIO::game::featHandler -- a class for handling feature elements

SYNOPSIS

This module is not used directly

DESCRIPTION

Bio::SeqIO::game::featHandler converts game XML <annotation> elements into flattened Bio::SeqFeature::Generic objects to be added to the sequence

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 one of 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 of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Sheldon McKay

Email mckays@cshl.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

  Title   : new
  Usage   : my $featHandler = Bio::SeqIO::game::featHandler->new($seq, $seq_h, $ann_l)
  Function: creates an object to deal with sequence features 
  Returns : a handler object
  Args    : $seq   -- a Bio::SeqI compliant object
            $seq_h -- ref. to a hash of other sequences associated 
                      with the main sequence (proteins, etc)
            $ann_l -- ref. to a list of annotations
 
 

add_source

  Title   : add_source
  Usage   : $featHandler->add_source($seq->length, \%tags);
  Function: creates a source feature
  Returns : a Bio::SeqFeature::Generic object 
  Args    : sequence length and a ref. to a hash of tag/value attributes
 
 

has_gene

  Title   : has_gene
  Usage   : my $gene = $self->_has_gene($gene, $gname, $id)
  Function: method to get/set the current gene feature
  Returns : a Bio::SeqFeature::Generic object (if there is a gene)
  Args    : (optional)
            $gene  -- an XML element for the annotation
            $gname -- gene name
            $id    -- gene ID (not always the same as the name)
 
 

_has_CDS

  Title   : _has_CDS
  Usage   : my $cds = $self->_has_CDS
  Function: internal getter/setter for CDS features
  Returns : a Bio::SeqFeature::Generic transcript object (or nothing)
  Args    : a Bio::SeqFeature::Generic transcript feature
 
 

add_annotation

  Title   : add_annotation
  Usage   : $featHandler->add_annotation($seq, $type, $id, $tags, $feats)
  Function: converts a containment hierarchy into an ordered list of flat features
  Returns : nothing
  Args    : $seq   -- a Bio::SeqI compliant object
            $type  -- the annotation type
            $id    -- the anotation ID
            $tags  -- ref. to a hash of tag/value attributes
            $feats -- ref to an array of Bio::SeqFeature::Generic objects
 
 

_add_generic_annotation

  Title   : _add_generic_annotation
  Usage   : $self->_add_generic_annotation($seq, $type, $id, $tags, $feats)
  Function: an internal method to handle non-gene annotations
  Returns : nothing
  Args    : $seq   -- a Bio::SeqI compliant object
            $type  -- the annotation type
            $id    -- the anotation ID
            $tags  -- ref. to a hash of tag/value attributes
            $feats -- ref to an array of Bio::SeqFeature::Generic objects
 
 

feature_set

  Title   : feature_set
  Usage   : push @feats, $featHandler->feature_set($id, $gname, $set, $anntype);
  Function: handles <feature_span> hierarchies (usually a transcript)
  Returns : a list of Bio::SeqFeature::Generic objects
  Args    : $id      -- ID of the feature set
            $gname   -- name of the gene
            $set     -- the <feature_set> object
            $anntype -- type of the parent annotation
 
 

_build_feature_set

  Title   : _build_feature_set
  Usage   : $self->_build_feature_set($set, 1) # 1 flag means retain the exon as a subfeat
  Function: an internal method to process attributes and subfeats of a feature set
  Returns : nothing
  Args    : $set -- a <feature_set> element
            1    -- optional flag to retain exons as subfeats.  Otherwise, they will
                    be converted to sublocations of a parent CDS feature
 
 

_add_feature_span

  Title   : _add_feature_span
  Usage   : $self->_add_feature_span($el, 1)
  Function: an internal method to process <feature_span> elements
  Returns : nothing
  Args    : $el -- a <feature_span> element
            1   -- an optional flag to retain exons as subfeatures
 
 

_add_CDS

  Title   : _add_CDS
  Usage   : my $cds = $self->_add_CDS($transcript, $tags)
  Function: an internal method to create a CDS feature from a transcript feature
  Returns : a Bio::SeqFeature::Generic object
  Args    : $transcript -- a Bio::SeqFeature::Generic object for a transcript
            $tags       -- ref. to a hash of tag/value attributes