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Manual Reference Pages  -  BIO::SEQIO::GAME::FEATHANDLER (3)

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NAME

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

CONTENTS

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:



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



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



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