module Bio::Blast::Remote::DDBJ
Remote BLAST factory using DDBJ Web API for Biology (xml.nig.ac.jp/).
Public Class Methods
new(program, db, options = [])
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Creates a remote BLAST factory using DDBJ. Returns Bio::Blast object.
Note for future improvement: In the future, it might return Bio::Blast::Remote::DDBJ or other object.
# File lib/bio/appl/blast/ddbj.rb, line 23 def self.new(program, db, options = []) Bio::Blast.new(program, db, options, 'ddbj') end
Public Instance Methods
exec_ddbj(query)
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executes BLAST and returns result as a string
# File lib/bio/appl/blast/ddbj.rb, line 103 def exec_ddbj(query) options = make_command_line_options opt = Bio::Blast::NCBIOptions.new(options) # REST objects are cached @ddbj_remote_blast ||= Bio::DDBJ::REST::Blast.new @ddbj_request_manager ||= Bio::DDBJ::REST::RequestManager.new program = opt.delete('-p') db = opt.delete('-d') optstr = Bio::Command.make_command_line_unix(opt.options) # using searchParamAsync qid = @ddbj_remote_blast.searchParamAsync(program, db, query, optstr) @output = qid result = @ddbj_request_manager.wait_getAsyncResult(qid) @output = result return @output end