Module Bio::Blast::Remote::DDBJ
In: lib/bio/appl/blast/ddbj.rb

Remote BLAST factory using DDBJ Web API for Biology (xml.nig.ac.jp/).

Methods

exec_ddbj   new  

Classes and Modules

Module Bio::Blast::Remote::DDBJ::Information

Public Class methods

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.

[Source]

    # File lib/bio/appl/blast/ddbj.rb, line 26
26:     def self.new(program, db, options = [])
27:       Bio::Blast.new(program, db, options, 'ddbj')
28:     end

Public Instance methods

executes BLAST and returns result as a string

[Source]

     # File lib/bio/appl/blast/ddbj.rb, line 106
106:     def exec_ddbj(query)
107:       options = make_command_line_options
108:       opt = Bio::Blast::NCBIOptions.new(options)
109: 
110:       # REST objects are cached
111:       @ddbj_remote_blast ||= Bio::DDBJ::REST::Blast.new
112:       @ddbj_request_manager ||= Bio::DDBJ::REST::RequestManager.new
113: 
114:       program = opt.delete('-p')
115:       db = opt.delete('-d')
116:       optstr = Bio::Command.make_command_line_unix(opt.options)
117: 
118:       # using searchParamAsync 
119:       qid = @ddbj_remote_blast.searchParamAsync(program, db, query, optstr)
120:       @output = qid
121: 
122:       result = @ddbj_request_manager.wait_getAsyncResult(qid)
123: 
124:       @output = result
125:       return @output
126:     end

[Validate]