| Bio::SeqIO::game::featHandler(3pm) | User Contributed Perl Documentation | Bio::SeqIO::game::featHandler(3pm) |
Bio::SeqIO::game::featHandler -- a class for handling feature elements
This module is not used directly
Bio::SeqIO::game::featHandler converts game XML <annotation> elements into flattened Bio::SeqFeature::Generic objects to be added to the sequence
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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)
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
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
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
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
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
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
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
| 2020-10-28 | perl v5.30.3 |