DAS::GUS::Segment::Feature -- a relative segment identified by a feature type
See DAS::GUS.
DAS::GUS::Segment::Feature is a stretch of sequence that corresponding to a single annotation in a GUS database.
It inherits from Bio::SeqFeatureI and so has the familiar start(), stop(), primary_tag() and location() methods (it implements Bio::LocationI too)
The remainder of this document describes the public and private methods implemented by this module.
Name: Haiming Wang Email: hwang@uga.edu
Title : new Usage : $f = DAS::GUS::Segment::Feature->new(@args); Function: create a new feature object Returns : new DAS::GUS::Segment::Feature object Args : see below Status : Internal
This method is called by DAS::GUS::Segment to create a new feature using information obtained from the GUS database.
The 12 arguments are positional:
$factory a DAS::GUS adaptor object $parent the parent feature object (if it exists) $srcseq the source sequence $start start of this feature $stop stop of this feature $type this feature's type (gene, arm, exon, etc) $score the feature's score $strand this feature's strand (relative to the source sequence, which has its own strandness!) $phase this feature's phase (often with respect to the previous feature in a group of related features) $group this feature's group information ?? $atts feature's attributes in $tag=$value format, use ? as delimiter $uniquename this feature's internal unique database name ?? $feature_id the feature's feature_id
This is called when creating a feature from scratch. It does not have an inherited coordinate system.
Title : feature_id Usage : $obj->feature_id($newval) Function: holds feature_id Returns : value of feature_id (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : group Usage : $group = $f->group([$new_group]); Function: Returns a feature name -- this is here to maintain backward compatibility with GFF and gbrowse. Returns : value of group (a scalar) Args :
Title : srcfeature_id Usage : $obj->srcfeature_id($newval) Function: Returns : value of srcfeature_id (a scalar) Args :
Title : strand Usage : $obj->strand() Function: Returns the strand of the feature. Unlike the other methods, the strand cannont be changed once the object is createed (due to coordinate considerations). Returns : -1, 0 or 1 ??? Args :
DAS::GUS::Segment::Feature implements the Bio::SeqFeatureI interface. Methods described below, Bio::SeqFeatureI for more details.
Title : attach_seq Usage : $sf->attch_seq($seq) Function: Attaches a Bio::Seq object to this feature. This Bio::Seq object is for the *entire* sequence: ie from 1 to 10000 Returns : TURE on success Args : a Bio::PrimarySeqI compliant object
Title : display_name Function: aliased to uniquename() for Bio::SeqFeatureI compatibility
Title : entire_seq Usage : $whole_seq = $sf->entire_seq() Function: gives the entire sequence that this seqfeature is attached to Returns : a Bio::PrimarySeqI compliant object, or undef is there is no sequence attached Args : none
Title : get_all_tags Function: aliased to all_tags() for Bio::SeqFeatureI compatibility
Title : get_SeqFeatures Function: aliased to sub_SeqFeature() for Bio::SeqFeatureI compatibility
Title : get_tag_values Usage : Function: Returns : Args :
Title : get_tagset_values Usage : Function: Returns : Args :
Title : gff_string Usage : $string = $feature->gff_string Function: return GFF3 representation of feature Returns : a string Args : none Status : Public
Title : has_tag Usage : Function: Returns : Args :
Title : primary_tag Usage : Function: aliased to type() for Bio::SeqFeatureI compatibility Returns : Args :
Title : seq_id Usage : $obj->seq_id($newval) Function: Returns : value of seq_id (a scalar) Args :
Title : source_tag Usage : Function: aliased to source() for Bio::SeqFeatureI compatibility Returns : Args :
Title : abs_strand Usage : $obj->abs_strand($newval) Function: aliased to strand() for backward compatibility Returns : Args :
Title : class Usage : Function: aliased to type() for backward compatibility Returns : Args :
Title : db_id Usage : Function: aliased to uniquename() for backward compatibility Returns : Args :
Title : factory Usage : $obj->factory($newval) Function: Returns : value of factory (a scalar) Args :
Title : id Usage : Function: Returns : Args :
Title : info Usage : Function: Returns : Args :
Title : length Usage : $obj->length() Function: convenience for end - start + 1 Returns : length of feature in basepairs Args : none
Title : method Usage : Function: Returns : Args :
Title : name Usage : Function: Returns : Args :
Title : parent Usage : $obj->parent($newval) Function: Returns : Args :
Title : score Usage : $obj->score($newval) Function: Returns : Args :
Title : all_tags Usage : Function: Returns : Args :
Title : source Usage : $source = $f->source([$newsource]) Function: get or set the feature source Returns : a string Args : a new source (optional) Status : Public
Title : segments Function: aliased to sub_SeqFeature() for compatibility
Title : subfeatures Usage : $obj->subfeatures($newval) Function: returns a list of subfeatures Returns : value of subfeatures (a scalar)
Title : sub_SeqFeature Usage : @feat = $feature->sub_SeqFeature([$type]) Function: get subfeatures Returns : a list of DAS::GUS::Segment::Feature objects Args : a feature method (optional) Status : Public
This method returns a list of any subfeatures that belong to the main feature. For those features that contain heterogeneous subfeatures, you can retrieve a subset of the subfeatures by providing a method name to filter on.
This method may also be called as segments() or get_SeqFeatures().
Title : add_subfeature Usage : $feature->add_subfeature($feature) Function: This method adds a new subfeature to the object. It is used internally by aggreagators, but is available for public use as well. Returns : nothing Args : a DAS::GUS::Segment::Feature object Status : Public
Title : location Usage : my $location = $seqfeature->location() Function: returns a location object suitable for identifying location of feature on sequence or parent feature Returns : Bio::LocationI object Args : none
Title : clone Usage : $feature = $f->clone Function: make a copy of the feature This method returns a copy of the feature. Returns : a new DAS::GUS::Segment::Feature object Args : none Status : Public
Title : sub_types Usage : @methods = $feature->sub_types Function: get methods of all sub_seqfeatures Returns : a list of method name Args : none Status : Public
For those features that contain subfeatures, this method will return a unique list of method names of thoese subfeatures, suitable for use with sub_SeqFeature()
Title : AUTOLOAD Usage : @subfeat = $feature->Method Function: Return subfeatures using autogenerated methods Returns : a list of DAS::GUS::Segment::Feature objects Args : none Status : Public
Any method that begins with an initial capital letter will be passed to AUTOLOAD and treated as a call to sub_SeqFeature with the method name used as the method argument. For instance, this call:
@exons = $feature->Exon;
is equivalent to this call:
@exons = $feature->sub_SeqFeature('exon');
Title : adjust_bounds Usage : $feature->adjust_bounds Function: adjust the bounds of a feature Returns : ($start,$stop,$strand) Args : none Status : Public
This method adjusts the boundaries of the feature to enclose all its subfeatures. It returns the new start, stop and strand of the enclosing feature.
Title : sort_features Usage : $feature->sort_features Function: sort features Returns : nothing Args : none Status : Public
This method sorts subfeatures in ascending order by their start position. For reverse strand features, it sorts subfeatures in descending order. After this is called sub_SeqFeature will return the features in order.
This method is called internally by merged_segments().
Title : asString Usage : $string = $feature->asString Function: return human-readabled representation of feature Returns : a string Args : none Status : Public
This method returns a human-readable representation of the feature and is called by the overloaded "" operator.
Title : attributes Usage : @attributes = $feature->attributes($name) Function: get the "attributes" on a particular feature Returns : an array of string Args : feature ID Status : Public
Two attributes have special meaning: "Note" is for backward compatibility and is used for unstructured text remarks. "Alias" is considered as a synonym for the feature name.
@gene_names = $feature->attributes('Gene'); @aliases = $feature->attributes('Alias');
If no name is provided, then attributes() returns a flattened hash, of attributes=>value pairs. This lets you do:
%attributes = $db->attributes;
Title : notes Usage : @notes = $feature->notes Function: get the "notes" on a particular feature Returns : an array of string Args : feature ID Status : Public
Title : aliases Usage : @aliases = $feature->aliaes Function: get the "aliases" on a particular feature Returns : an array of string Args : feature ID Status : Public
This method will return a list of attributes of type 'Alias'.
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