Method: Bio::Blast#initialize

Defined in:

lib/bio/appl/blast.rb

#initialize(program, db, opt = [], server = 'local') ⇒ Blast

Creates a Bio::Blast factory object.

To run any BLAST searches, a factory has to be created that describes a certain BLAST pipeline: the program to use, the database to search, any options and the server to use. E.g.

blast_factory = Bio::Blast.new('blastn','dbsts', '-e 0.0001 -r 4', 'genomenet')

---

Arguments:

• program (required): ‘blastn’, ‘blastp’, ‘blastx’, ‘tblastn’ or ‘tblastx’

• db (required): name of the (local or remote) database

• options: blastall options \

(see www.genome.jp/dbget-bin/show_man?blast2)

• server: server to use (e.g. ‘genomenet’; DEFAULT = ‘local’)

Returns

Bio::Blast factory object

# File 'lib/bio/appl/blast.rb', line 317

def initialize(program, db, opt = [], server = 'local')
  @program  = program
  @db       = db

  @blastall = 'blastall'
  @matrix   = nil
  @filter   = nil

  @output   = ''
  @parser   = nil
  @format   = nil

  @options = set_options(opt, program, db)
  self.server = server
end