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 23
23:     def self.new(program, db, options = [])
24:       Bio::Blast.new(program, db, options, 'ddbj')
25:     end

Public Instance methods

executes BLAST and returns result as a string

[Source]

     # File lib/bio/appl/blast/ddbj.rb, line 103
103:     def exec_ddbj(query)
104:       options = make_command_line_options
105:       opt = Bio::Blast::NCBIOptions.new(options)
106: 
107:       # REST objects are cached
108:       @ddbj_remote_blast ||= Bio::DDBJ::REST::Blast.new
109:       @ddbj_request_manager ||= Bio::DDBJ::REST::RequestManager.new
110: 
111:       program = opt.delete('-p')
112:       db = opt.delete('-d')
113:       optstr = Bio::Command.make_command_line_unix(opt.options)
114: 
115:       # using searchParamAsync 
116:       qid = @ddbj_remote_blast.searchParamAsync(program, db, query, optstr)
117:       @output = qid
118: 
119:       result = @ddbj_request_manager.wait_getAsyncResult(qid)
120: 
121:       @output = result
122:       return @output
123:     end

[Validate]