Class | Bio::Fasta |
In: |
lib/bio/appl/fasta.rb
lib/bio/appl/fasta/format10.rb |
Parent: | Object |
db | [RW] | |
format | [R] | |
ktup | [RW] | |
matrix | [RW] | |
options | [RW] | |
output | [R] | Returns a String containing fasta execution output in as is format. |
program | [RW] | |
server | [RW] |
Returns a FASTA factory object (Bio::Fasta) to run FASTA search on local computer.
# File lib/bio/appl/fasta.rb, line 80 80: def self.local(program, db, option = '') 81: self.new(program, db, option, 'local') 82: end
Returns a FASTA factory object (Bio::Fasta).
# File lib/bio/appl/fasta.rb, line 23 23: def initialize(program, db, opt = [], server = 'local') 24: @format = 10 25: 26: @program = program 27: @db = db 28: @server = server 29: 30: @ktup = nil 31: @matrix = nil 32: 33: @output = '' 34: 35: begin 36: a = opt.to_ary 37: rescue NameError #NoMethodError 38: # backward compatibility 39: a = Shellwords.shellwords(opt) 40: end 41: @options = [ '-Q', '-H', '-m', @format.to_s, *a ] # need -a ? 42: 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 74: def self.parser(parser) 75: warn 'Bio::Fasta.parser is obsoleted and will soon be removed.' 76: 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 90: def self.remote(program, db, option = '', server = 'genomenet') 91: self.new(program, db, option, server) 92: end
# File lib/bio/appl/fasta.rb, line 48 48: def option 49: # backward compatibility 50: Bio::Command.make_command_line(@options) 51: end
# File lib/bio/appl/fasta.rb, line 53 53: def option=(str) 54: # backward compatibility 55: @options = Shellwords.shellwords(str) 56: end
Execute FASTA search and returns Report object (Bio::Fasta::Report).
# File lib/bio/appl/fasta.rb, line 95 95: def query(query) 96: return self.send("exec_#{@server}", query.to_s) 97: end