NAME
Bio::Chado::Schema::Result::Genetic::Genotype
DESCRIPTION
Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.
ACCESSORS
genotype_id
data_type: 'integer'
is_auto_increment: 1
is_nullable: 0
sequence: 'genotype_genotype_id_seq'name
data_type: 'text'
is_nullable: 1Optional alternative name for a genotype, for display purposes.
uniquename
data_type: 'text'
is_nullable: 0The unique name for a genotype; typically derived from the features making up the genotype.
description
data_type: 'varchar'
is_nullable: 1
size: 255type_id
data_type: 'integer'
is_foreign_key: 1
is_nullable: 0RELATIONS
feature_genotypes
Type: has_many
Related object: Bio::Chado::Schema::Result::Genetic::FeatureGenotype
type
Type: belongs_to
Related object: Bio::Chado::Schema::Result::Cv::Cvterm
genotypeprops
Type: has_many
Related object: Bio::Chado::Schema::Result::Genetic::Genotypeprop
nd_experiment_genotypes
Type: has_many
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentGenotype
phendescs
Type: has_many
Related object: Bio::Chado::Schema::Result::Genetic::Phendesc
phenotype_comparison_genotype1s
Type: has_many
Related object: Bio::Chado::Schema::Result::Genetic::PhenotypeComparison
phenotype_comparison_genotype2s
Type: has_many
Related object: Bio::Chado::Schema::Result::Genetic::PhenotypeComparison
phenstatements
Type: has_many
Related object: Bio::Chado::Schema::Result::Genetic::Phenstatement
stock_genotypes
Type: has_many
Related object: Bio::Chado::Schema::Result::Stock::StockGenotype
create_genotypeprops
Usage: $set->create_genotypeprops({ baz => 2, foo => 'bar' });
Desc : convenience method to create genotype 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 genotypeprop name. Default false.
cv_name => cv.name to use for the given genotypeprops.
Defaults to 'genotype_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
rank => force numeric rank. Be careful not to pass ranks that already exist
for the property type. The function will die in such case.
allow_duplicate_values => default false.
If true, allow duplicate instances of the same genotype
and value in the properties of the genotype. Duplicate
values will have different ranks.
}
Ret : hashref of { propname => new genotypeprop object }