Bio::Chado::Schema::Result::Stock::Stock
Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.
data_type: 'integer' is_auto_increment: 1 is_nullable: 0 sequence: 'stock_stock_id_seq'
data_type: 'integer' is_foreign_key: 1 is_nullable: 1
The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref.
The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined.
data_type: 'varchar' is_nullable: 1 size: 255
The name is a human-readable local name for a stock.
data_type: 'text' is_nullable: 0
data_type: 'text' is_nullable: 1
The description is the genetic description provided in the stock list.
data_type: 'integer' is_foreign_key: 1 is_nullable: 0
The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm.
data_type: 'boolean' default_value: false is_nullable: 0
Type: has_many
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentStock
Type: belongs_to
Related object: Bio::Chado::Schema::Result::General::Dbxref
Related object: Bio::Chado::Schema::Result::Cv::Cvterm
Related object: Bio::Chado::Schema::Result::Organism::Organism
Related object: Bio::Chado::Schema::Result::Stock::StockcollectionStock
Related object: Bio::Chado::Schema::Result::Stock::StockCvterm
Related object: Bio::Chado::Schema::Result::Stock::StockDbxref
Related object: Bio::Chado::Schema::Result::Stock::StockGenotype
Related object: Bio::Chado::Schema::Result::Stock::Stockprop
Related object: Bio::Chado::Schema::Result::Stock::StockPub
Related object: Bio::Chado::Schema::Result::Stock::StockRelationship
Usage: $set->create_stockprops({ baz => 2, foo => 'bar' }); Desc : convenience method to create stock 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 stockprop name. Default false. cv_name => cv.name to use for the given stockprops. Defaults to 'stock_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 stock and value in the properties of the stock. Duplicate values will have different ranks. } Ret : hashref of { propname => new stockprop object }
Usage: $schema->resultset("Stock::Stock")->stock_phenotypes_rs($stock_rs); Desc: retrieve a resultset for stock(s) with phenotyping experiments with the following values mapped to [column name] stock_id [stock_id] phenotype.value [value] observable.name [observable] (the cvterm name for the phenotype.observable field) observable_cvterm_id [observable_id] observable.definition [definition] unit_name (from phenotype_cvterm) cv_name (the cv_name for the phenotype_cvterm) type_name (the cvterm name for the phenotype_cvterm) method_name (a phenotypeprop value) dbxref.accession [accession] of the observable cvterm db.name of the observable cvterm [db_name] (useful for constructing the ontology ID of the observable) project.description [project_description] (useful for grouping phenotype values by projects) Args: a L<Bio::Chado::Schema::Result::Stock::Stock> resultset Ret: a resultset with the above columns. Access the data with e.g. $rs->get_column('stock_id')
Usage: $schema->resultset("Stock::Stock")->recursive_phenotypes_rs($stock_rs, \@results) Desc: Retrieve recursively phenotypes of stock objects and their subjects Args: Stock resultSet and an arrayref with the results Ret: listref of stock_phenotypes_rs (see function stock_phenotypes_rs for columns fetched)
Usage: $schema->resultset("Stock::Stock")->stock_genotypes_rs($stock_rs); Desc: retrieve a resultset for stock(s) with genotyping experiments with the following values mapped to [column name] stock_id [stock_id] genotype.name [name] genotype.uniquname [uniquename] genotype.description [description] genotype.type.name [type_name] (the cvterm name for the genotype type) propvalue [propvalue] (a genotypeprop value) Args: a L<Bio::Chado::Schema::Result::Stock::Stock> resultset Ret: a resultset with the above columns. Access the data with e.g. $rs->get_column('stock_id')
Usage: $schema->resultset("Stock::Stock")->stock_project_phenotypes($stock_rs); Desc: retrieve a list of phenotype resultsets by project name Args: a L<Bio::Chado::Schema::Result::Stock::Stock> object or a stock resultset Ret: hashref key = project descriptions, values = hash ref of {phenotypes} = phenotype resultset {project} = L<Bio::Chado::Schema::Result::Project::Project> object
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.