Bio::Chado::Schema::Sequence::Feature
A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on; see the Sequence Ontology for more. The combination of organism_id, uniquename and type_id should be unique.
data_type: 'integer' is_auto_increment: 1 is_nullable: 0 sequence: 'feature_feature_id_seq'
data_type: 'integer' is_foreign_key: 1 is_nullable: 1
An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref.
data_type: 'integer' is_foreign_key: 1 is_nullable: 0
The organism to which this feature belongs. This column is mandatory.
data_type: 'varchar' is_nullable: 1 size: 255
The optional human-readable common name for a feature, for display purposes.
data_type: 'text' is_nullable: 0
The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism.
data_type: 'text' is_nullable: 1
A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.
data_type: 'integer' is_nullable: 1
The length of the residue feature. See column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known.
data_type: 'char' is_nullable: 1 size: 32
The 32-character checksum of the sequence, calculated using the MD5 algorithm. This is practically guaranteed to be unique for any feature. This column thus acts as a unique identifier on the mathematical sequence.
A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table.
data_type: 'boolean' default_value: false is_nullable: 0
Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis and annotation may be fuzzy, this should be determined on a per-project basis in a consistent manner. One requirement is that there should only be one non-analysis version of each wild-type gene feature in a genome, whereas the same gene feature can be predicted multiple times in different analyses.
Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.
data_type: 'timestamp' default_value: current_timestamp is_nullable: 0 original: {default_value => \"now()"}
For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.
Type: has_many
Related object: Bio::Chado::Schema::Companalysis::Analysisfeature
Related object: Bio::Chado::Schema::CellLine::CellLineFeature
Related object: Bio::Chado::Schema::Mage::Element
Type: belongs_to
Related object: Bio::Chado::Schema::Cv::Cvterm
Related object: Bio::Chado::Schema::General::Dbxref
Related object: Bio::Chado::Schema::Organism::Organism
Related object: Bio::Chado::Schema::Sequence::FeatureCvterm
Related object: Bio::Chado::Schema::Sequence::FeatureDbxref
Related object: Bio::Chado::Schema::Expression::FeatureExpression
Related object: Bio::Chado::Schema::Genetic::FeatureGenotype
Related object: Bio::Chado::Schema::Sequence::Featureloc
Related object: Bio::Chado::Schema::Phenotype::FeaturePhenotype
Related object: Bio::Chado::Schema::Map::Featurepos
Related object: Bio::Chado::Schema::Sequence::Featureprop
Related object: Bio::Chado::Schema::Sequence::FeaturePub
Related object: Bio::Chado::Schema::Map::Featurerange
Related object: Bio::Chado::Schema::Sequence::FeatureRelationship
Related object: Bio::Chado::Schema::Sequence::FeatureSynonym
Related object: Bio::Chado::Schema::Library::LibraryFeature
Related object: Bio::Chado::Schema::Phylogeny::Phylonode
Related object: Bio::Chado::Schema::Mage::StudypropFeature
Type: has_to_many
Returns a list of parent relationships.
Returns a list of child relationships.
Alias for dbxref
Type: many_to_many
Returns a list of parent features.
Related object: Bio::Chado::Schema::Sequence::Feature
Returns a list of child features.
Related object: Bio::Chado::Schema::General::Dbxref (i.e. dbxref table) Bio::Chado::Schema::Sequence::FeatureDbxref (feature_dbxref table)
Alias for dbxrefs_mm
Usage: $set->create_featureprops({ baz => 2, foo => 'bar' }); Desc : convenience method to create feature properties using cvterms from the ontology with the given name Args : hashref of { propname => value, ...}, options hashref as: { autocreate => 0, (optional) boolean, if passed, automatically create cv, cvterm, and dbxref rows if one cannot be found for the given featureprop name. Default false. cv_name => cv.name to use for the given featureprops. Defaults to 'feature_property', db_name => db.name to use for autocreated dbxrefs, default 'null', dbxref_accession_prefix => optional, default 'autocreated:', definitions => optional hashref of: { cvterm_name => definition, } to load into the cvterm table when autocreating cvterms allow_duplicate_values => default false. If true, allow duplicate instances of the same cvterm and value in the properties of the feature. Duplicate values will have different ranks. } Ret : hashref of { propname => new featureprop object }
Status : public Usage : $feat->search_featureprops( 'description' ) # OR $feat->search_featureprops({ name => 'description'}) Returns : DBIx::Class::ResultSet like other search() methods Args : single string to match cvterm name, or hashref of search criteria. This is passed to $chado->resultset('Cv::Cvterm') ->search({ your criteria }) Convenience method to search featureprops for a feature that match to Cvterms having the given criterion hash
The methods below are intended to provide some compatibility with BioPerl's Bio::PrimarySeqI interface, so that a feature may be used as a sequence. Note that Bio::PrimarySeqI only provides identifier, accession, and sequence information, no subfeatures, ranges, or the like.
Support for BioPerl's more complete Bio::SeqI interface, which includes those things, still needs to be implemented. If you are interested in helping with this, please contact GMOD!
These are aliases for name(), which just returns the contents of the feature.name field
Alias for $feature->residues()
Usage: say $feature->accession_number Desc : get an "<accession>.<version>"-style string. gets this from either the primary dbxref, or the first secondary_dbxref found Args : none Ret : string of the form "accession.version" formed from the accession and version fields of either the primary or secondary dbxrefs
No arguments, returns the seqlen(), or length( $feature->residues ) if that is not defined.
No arguments, returns the value of the first 'description' featureprop found for this feature.
Not implemented. Throws an error if used.
To install Bio::Chado::Schema, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Chado::Schema
CPAN shell
perl -MCPAN -e shell install Bio::Chado::Schema
For more information on module installation, please visit the detailed CPAN module installation guide.