| Bio::Chado::Schema::Sequence::Feature |
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.
Bio::Chado::Schema::Sequence::Feature
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.
data_type: 'integer' is_foreign_key: 1 is_nullable: 0
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.
data_type: 'boolean' default_value: false is_nullable: 0
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.
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: the Bio::Chado::Schema::Companalysis::Analysisfeature manpage
Type: has_many
Related object: the Bio::Chado::Schema::CellLine::CellLineFeature manpage
Type: has_many
Related object: the Bio::Chado::Schema::Mage::Element manpage
Type: belongs_to
Related object: the Bio::Chado::Schema::Cv::Cvterm manpage
Type: belongs_to
Related object: the Bio::Chado::Schema::General::Dbxref manpage
Type: belongs_to
Related object: the Bio::Chado::Schema::Organism::Organism manpage
Type: has_many
Related object: the Bio::Chado::Schema::Sequence::FeatureCvterm manpage
Type: has_many
Related object: the Bio::Chado::Schema::Sequence::FeatureDbxref manpage
Type: has_many
Related object: the Bio::Chado::Schema::Expression::FeatureExpression manpage
Type: has_many
Related object: the Bio::Chado::Schema::Genetic::FeatureGenotype manpage
Type: has_many
Related object: the Bio::Chado::Schema::Genetic::FeatureGenotype manpage
Type: has_many
Related object: the Bio::Chado::Schema::Sequence::Featureloc manpage
Type: has_many
Related object: the Bio::Chado::Schema::Sequence::Featureloc manpage
Type: has_many
Related object: the Bio::Chado::Schema::Phenotype::FeaturePhenotype manpage
Type: has_many
Related object: the Bio::Chado::Schema::Map::Featurepos manpage
Type: has_many
Related object: the Bio::Chado::Schema::Map::Featurepos manpage
Type: has_many
Related object: the Bio::Chado::Schema::Sequence::Featureprop manpage
Type: has_many
Related object: the Bio::Chado::Schema::Sequence::FeaturePub manpage
Type: has_many
Related object: the Bio::Chado::Schema::Map::Featurerange manpage
Type: has_many
Related object: the Bio::Chado::Schema::Map::Featurerange manpage
Type: has_many
Related object: the Bio::Chado::Schema::Map::Featurerange manpage
Type: has_many
Related object: the Bio::Chado::Schema::Map::Featurerange manpage
Type: has_many
Related object: the Bio::Chado::Schema::Map::Featurerange manpage
Type: has_many
Related object: the Bio::Chado::Schema::Sequence::FeatureRelationship manpage
Type: has_many
Related object: the Bio::Chado::Schema::Sequence::FeatureRelationship manpage
Type: has_many
Related object: the Bio::Chado::Schema::Sequence::FeatureSynonym manpage
Type: has_many
Related object: the Bio::Chado::Schema::Library::LibraryFeature manpage
Type: has_many
Related object: the Bio::Chado::Schema::Phylogeny::Phylonode manpage
Type: has_many
Related object: the Bio::Chado::Schema::Mage::StudypropFeature manpage
Type: has_to_many
Returns a list of parent relationships.
Related object: Bio::Chado::Schema::Sequence::FeatureRelationship
Type: has_to_many
Returns a list of child relationships.
Related object: Bio::Chado::Schema::Sequence::FeatureRelationship
Alias for dbxref
Type: many_to_many
Returns a list of parent features.
Related object: Bio::Chado::Schema::Sequence::Feature
Type: many_to_many
Returns a list of child features.
Related object: Bio::Chado::Schema::Sequence::Feature
Type: many_to_many
Related object: the Bio::Chado::Schema::General::Dbxref manpage (i.e. dbxref table) the Bio::Chado::Schema::Sequence::FeatureDbxref manpage (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 the Bio::PrimarySeqI manpage interface, so that a feature may be used as a sequence. Note that the Bio::PrimarySeqI manpage only provides identifier, accession, and sequence information, no subfeatures, ranges, or the like.
Support for BioPerl's more complete the Bio::SeqI manpage 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.
Robert Buels <rbuels@cpan.org>
This software is copyright (c) 2009 by Robert Buels.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.
| Bio::Chado::Schema::Sequence::Feature |