Bio::DB::Das::Chado::Segment::Feature
See Bio::DB::Das::Chado.
Not yet written
Title : new Usage : $f = Bio::DB::Das::Chado::Segment::Feature->new(@args); Function: create a new feature object Returns : new Bio::DB::Das::Chado::Segment::Feature object Args : see below Status : Internal
This method is called by Bio::DB::Das::Chado::Segment to create a new feature using information obtained from the chado database.
The 11 arguments are positional:
$factory a Bio::DB::Das::Chado adaptor object (or descendent) $parent the parent feature object (if it exists) $srcseq the source sequence $start start of this feature $stop stop of this feature $type a Bio::DB::GFF::Typename (containing a method and source) $score the feature's score $strand this feature's strand (relative to the source sequence, which has its own strandedness!) $phase this feature's phase (often with respect to the previous feature in a group of related features) $group this feature's featureloc.locgroup (NOT a GFF holdover) $uniquename this feature's internal unique database name (feature.uniquename) $feature_id the feature's feature_id
This is called when creating a feature from scratch. It does not have an inherited coordinate system.
Methods below are accessors for data that is drawn directly from the Chado database and can be considered "primary" accessors for this class.
Title : feature_id Usage : $obj->feature_id($newval) Function: holds feature.feature_id Returns : value of feature_id (a scalar) Args : on set, new value (a scalar or undef, optional)
Implemented in Bio::DB::Das::Chado::Segment
$obj->organism() #get existing value $obj->organism($newval) #set new value
value of organism (a scalar)
new value of organism (to set)
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 : on set, new value (a scalar or undef, optional)
Title : srcfeature_id Usage : $obj->srcfeature_id($newval) Function: ??? Returns : value of srcfeature_id (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : strand Usage : $obj->strand() Function: Returns the strand of the feature. Unlike the other methods, the strand cannot be changed once the object is created (due to coordinate considerations). corresponds to featureloc.strand Returns : -1, 0, or 1 Args : on set, new value (a scalar or undef, optional)
$obj->phase() #get existing value $obj->phase($newval) #set new value
value of phase (a scalar)
new value of phase (to set)
Title : type Usage : $obj->type($newval) Function: holds a Bio::DB::GFF::Typename object Returns : returns a Bio::DB::GFF::Typename object Args : on set, new value
Title : uniquename Usage : $obj->uniquename($newval) Function: holds feature.uniquename Returns : value of uniquename (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : is_analysis Usage : $obj->is_analysis($newval) Function: holds feature.is_analysis Returns : value of is_analysis (a scalar) Args : on set, new value (a scalar or undef, optional)
Bio::DB::Das::Chado::Segment::Feature implements the Bio::SeqFeatureI interface. Methods described below, see Bio:SeqFeatureI for more details.
Title : attach_seq Usage : $sf->attach_seq($seq) Function: Attaches a Bio::Seq object to this feature. This Bio::Seq object is for the *entire* sequence: ie from 1 to 10000 Example : Returns : TRUE 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 Example : Returns : a Bio::PrimarySeqI compliant object, or undef if 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 : $feature->get_tag_values Function: Returns values associated with a particular tag Returns : A list of values Args : A string (the name of the tag)
Title : get_tagset_values Usage : Function: ??? Returns : Args :
Title : gff_string Usage : Function: ??? Returns : Args :
Title : has_tag Usage : Function: ??? Returns : Args :
Title : primary_tag Function: aliased to type() for Bio::SeqFeatureI compatibility
Title : seq Usage : Function: ??? Returns : Args :
Title : seq_id Usage : $obj->seq_id($newval) Function: Set or get the name of the reference sequence that the feature resides on. Returns : value of seq_id (a scalar) Args : on set, new value (a scalar or undef, optional)
Bio::SeqFeatureI in turn ISA Bio::RangeI. Bio::RangeI interface methods described below, Bio::RangeI for details.
Title : end Function: inherited, L<Bio::DB::Das::Chado::Segment>
Title : start Function: inherited, L<Bio::DB::Das::Chado::Segment>
Title : strand Function: inherited, L<Bio::DB::Das::Chado::Segment>
Title : abs_strand Usage : $obj->abs_strand($newval) Function: aliased to strand() for backward compatibility
Title : db_id Function: aliased to uniquename() for backward compatibility
Title : factory Usage : $obj->factory($newval) Function: ??? Returns : value of factory (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : id Function: aliased to uniquename() for backward compatibility
Title : info Function: aliased to uniquename() for backward compatibility with broken generic glyphs primarily
Title : length Usage : $obj->length() Function: convenience for end - start + 1 Returns : length of feature in basepairs Args : none
Title : method Usage : $obj->method Function: returns a Feature's method (SOFA type) Returns : the Features SOFA type Args : none
Title : name Function: aliased to group for backward compatibility
Title : parent Usage : $obj->parent($newval) Function: ??? Returns : value of parent (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : score Usage : $obj->score($newval) Function: holds the (alignment?) feature's score Returns : value of score (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : target Usage : $feature->target Function: returns a Bio::DB::Das::Chado::Segment that corresponds to the target of a similarity pair Returns : a Bio::DB::Das::Chado::Segment object Args : none
Title : all_tags Usage : Function: ??? Returns : Args :
Title : source Usage : $f->source(); Function: caches and returns the source from a GFF file, this is stored in dbxref with a db of 'GFF_Source' Returns : See above Args : none
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) FIXME THIS SHOULD RETURN A LIST OR AN ARRAY AND BE DOCUMENTED AS SUCH NOT RETURN AN ARRAYREF OR HASHREF. FOR ADDING/SETTING ELEMENTS WE NEED ADD_ AND SET_ METHODS Args : on set, new value (a scalar or undef, optional)
Title : sub_SeqFeature Usage : @feat = $feature->sub_SeqFeature([$type]) Function: 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 an array of types to filter on. For AcePerl compatibility, this method may also be called as segments(). Returns : a list of Bio::DB::Das::Chado::Segment::Feature objects Args : a feature method (optional) Status : Public
dgg: polypeptide or protein is a most important feature, don't drop it! This is the part of a gene that has lots of attached critical info: protein ID, translation, GO terms, Dbxrefs to other proteins) While this exclusion fixes a display bug, e.g. Glyph/processed_transcript it is much less problematic to patch the glyph displayers. elsif ( 0 && $inferCDS) { #just remove polypeptide features my @ok_feats = grep {$_->type->method ne 'polypeptide'} @features; warn @ok_feats if DEBUG; return @ok_feats; }
$obj->_do_the_inferring(@features)
Takes a list of polypeptide and exon features and infers CDS and UTR features from them.
A list of CDS and UTR features
A list of polypeptide and exon features
This function will break with polycistronic genes, as there will be more than one polypeptide per set of exons, and this function assumes that there is only one.
Title : _calc_phases Usage : $feature->_calc_phases(@exons) Function: calculstes phases for exons without phases Returns : a list of exon feature objects with phases Args : a list of sorted (by transcription order) exons Status : private
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 : add_subfeature Usage : $feature->add_subfeature($feature) Function: This method adds a new subfeature to the object. It is used internally by aggregators, but is available for public use as well. Returns : nothing Args : a Bio::DB::Das::Chado::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 Returns : a new Bio::DB::Das::Chado::Segment::Feature object Args : none Status : Public
This method returns a copy of the feature.
Title : sub_types Usage : @methods = $feature->sub_types Function: get methods of all sub-seqfeatures Returns : a list of method names Args : none Status : Public
For those features that contain subfeatures, this method will return a unique list of method names of those subfeatures, suitable for use with sub_SeqFeature().
Title : AUTOLOAD Usage : @subfeat = $feature->Method Function: Return subfeatures using autogenerated methods Returns : a list of Bio::DB::Das::Chado::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 : synonyms Usage : @synonyms = $feature->synonyms Function: return a list of synonyms for a feature Returns : a list of strings Args : none Status : Public
Looks in the synonym table to collect all synonyms of a feature.
Title : cmap_link Usage : $link = $feature->cmap_link Function: returns a URL link to the corresponding feature in cmap Returns : a string Args : none Status : Public
Returns a link to a cmap installation (which is assumed to be on the same host as gbrowse). In addition to the cmap tables being present in chado, this method also assumes the presence of a link table called feature_to_cmap. See the cmap documentation for more information.
This function is intended primarily to be used in gbrowse conf files. For example:
link = sub {my $self = shift; return $self->cmap_link();}
2 POD Errors
The following errors were encountered while parsing the POD:
'=item' outside of any '=over'
You forgot a '=back' before '=head2'
To install Bio::DB::Das::Chado, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::DB::Das::Chado
CPAN shell
perl -MCPAN -e shell install Bio::DB::Das::Chado
For more information on module installation, please visit the detailed CPAN module installation guide.