Class: Bio::SQL
- Defined in:
- lib/bio/io/sql.rb,
lib/bio/db/biosql/sequence.rb
Defined Under Namespace
Classes: Sequence
Class Method Summary collapse
- .delete_entry_accession(accession) ⇒ Object
- .delete_entry_id(id) ⇒ Object
- .exists_accession(accession) ⇒ Object
- .exists_database(name) ⇒ Object
- .fetch_accession(accession) ⇒ Object
- .fetch_id(id) ⇒ Object
- .list_databases ⇒ Object
- .list_entries ⇒ Object
Class Method Details
.delete_entry_accession(accession) ⇒ Object
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# File 'lib/bio/io/sql.rb', line 73 def self.delete_entry_accession(accession) Bio::SQL::Bioentry.find_by_accession(accession.upcase).destroy! end |
.delete_entry_id(id) ⇒ Object
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# File 'lib/bio/io/sql.rb', line 69 def self.delete_entry_id(id) Bio::SQL::Bioentry.delete(id) end |
.exists_accession(accession) ⇒ Object
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# File 'lib/bio/io/sql.rb', line 47 def self.exists_accession(accession) # Bio::SQL::Bioentry.find_by_accession(accession.upcase).nil? ? false : true !Bio::SQL::Bioentry.find_by_accession(accession.upcase).nil? end |
.exists_database(name) ⇒ Object
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# File 'lib/bio/io/sql.rb', line 52 def self.exists_database(name) # Bio::SQL::Biodatabase.find_by_name(name).nil? ? false : true !Bio::SQL::Biodatabase.first(:name=>name).nil? end |
.fetch_accession(accession) ⇒ Object
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# File 'lib/bio/io/sql.rb', line 42 def self.fetch_accession(accession) # Bio::SQL::Bioentry.exists?(:accession => accession) ? Bio::SQL::Sequence.new(:entry=>Bio::SQL::Bioentry.find_by_accession(accession)) : nil Bio::SQL::Sequence.new(:entry=>Bio::SQL::Bioentry.find_by_accession(accession.upcase)) end |
.fetch_id(id) ⇒ Object
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# File 'lib/bio/io/sql.rb', line 38 def self.fetch_id(id) Bio::SQL::Bioentry.find(id) end |