Class: Bio::SQL

Inherits:
Object show all
Defined in:
lib/bio/io/sql.rb,
lib/bio/db/biosql/sequence.rb

Defined Under Namespace

Classes: Sequence

Class Method Summary collapse

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

.list_databases ⇒ Object 



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# File 'lib/bio/io/sql.rb', line 63

def self.list_databases
  Bio::SQL::Biodatabase.all.collect do|entry|
    {:id=>entry.biodatabase_id, :name => entry.name}
  end
end

.list_entries ⇒ Object 



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# File 'lib/bio/io/sql.rb', line 57

def self.list_entries
  Bio::SQL::Bioentry.all.collect do|entry|
    {:id=>entry.bioentry_id, :accession=>entry.accession}
  end
end