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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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:

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

AUTHOR - Sheldon McKay

Email [email protected]

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