Returns a FASTA factory object (Bio::Fasta) to run FASTA search on local computer.
# File lib/bio/appl/fasta.rb, line 80 def self.local(program, db, option = '') self.new(program, db, option, 'local') end
Returns a FASTA factory object (Bio::Fasta).
# File lib/bio/appl/fasta.rb, line 23 def initialize(program, db, opt = [], server = 'local') @format = 10 @program = program @db = db @server = server @ktup = nil @matrix = nil @output = '' begin a = opt.to_ary rescue NameError #NoMethodError # backward compatibility a = Shellwords.shellwords(opt) end @options = [ '-Q', '-H', '-m', @format.to_s, *a ] # need -a ? end
OBSOLETE. Does nothing and shows warning messages.
Historically, selecting parser to use ('format6' or 'format10' were expected, but only 'format10' was available as a working parser).
# File lib/bio/appl/fasta.rb, line 74 def self.parser(parser) warn 'Bio::Fasta.parser is obsoleted and will soon be removed.' end
Returns a FASTA factory object (Bio::Fasta) to execute FASTA search on remote server.
For the develpper, you can add server 'hoge' by adding exec_hoge(query) method.
# File lib/bio/appl/fasta.rb, line 90 def self.remote(program, db, option = '', server = 'genomenet') self.new(program, db, option, server) end
Accessors for the -m option.
# File lib/bio/appl/fasta.rb, line 59 def format=(num) @format = num.to_i if i = @options.index('-m') then @options[i+1, 1] = @format.to_s else @options << '-m' << @format.to_s end end
# File lib/bio/appl/fasta.rb, line 48 def option # backward compatibility Bio::Command.make_command_line(@options) end
# File lib/bio/appl/fasta.rb, line 53 def option=(str) # backward compatibility @options = Shellwords.shellwords(str) end
Execute FASTA search and returns Report object (Bio::Fasta::Report).
# File lib/bio/appl/fasta.rb, line 95 def query(query) return self.send("exec_#{@server}", query.to_s) end
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