/ 
BioPerl-1.007001
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SeqIO::game::featHandler

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:

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