Class | Bio::PSORT::PSORT1 |
In: |
lib/bio/appl/psort.rb
lib/bio/appl/psort/report.rb |
Parent: | Object |
Bio::PSORT::PSORT1 is a wapper class for the original PSORT program.
serv = Bio::PSORT::PSORT1.imsut serv.title = 'Query_title_splited_by_white space' serv.exec(seq, false) # seq.class => String serv.exec(seq) report = serv.exec(Bio::FastaFormat.new(seq)) report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
origin | [RW] |
An accessor of the origin argument. Default setting is "yeast".
Usable values:
|
sequence | [RW] | An accessor of the query sequence argument. |
title | [RW] | An accessor of the title argument. Default setting is ‘MYSEQ’. The value is automatically setted if you use a query in Bio::FastaFormat. |
Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote) connecting to the IMSUT server.
# File lib/bio/appl/psort.rb, line 178 178: def self.imsut 179: self.new(Remote.new(ServerURI[:IMSUT][:PSORT1])) 180: end
Sets a cgi client (Bio::PSORT::PSORT1::Remote).
# File lib/bio/appl/psort.rb, line 199 199: def initialize(driver, origin = 'yeast', title = 'MYSEQ') 200: @serv = driver 201: @origin = origin # Gram-positive bacterium, Gram-negative bacterium, 202: # yeast, aminal, plant 203: @title = title 204: @sequence = '' 205: end
Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote) connecting to the NIBB server.
# File lib/bio/appl/psort.rb, line 185 185: def self.okazaki 186: self.new(Remote.new(ServerURI[:Okazaki][:PSORT1])) 187: end
Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote) connecting to the Peking server.
# File lib/bio/appl/psort.rb, line 192 192: def self.peking 193: self.new(Remote.new(ServerURI[:Peking][:PSORT1])) 194: end
Executes the query (faa) and returns an Bio::PSORT::PSORT1::Report.
The ``faa’’ argument is acceptable a sequence both in String and in Bio::FastaFormat.
If you set the second argument is ``parsing = false’’, returns ourput text without any parsing.
# File lib/bio/appl/psort.rb, line 233 233: def exec(faa, parsing = true) 234: if faa.class == Bio::FastaFormat 235: @title = faa.entry_id if @title == 'MYSEQ' 236: @sequence = faa.seq 237: @serv.args = {'title' => @title, 'origin' => @origin} 238: @serv.parsing = parsing 239: return @serv.exec(sequence) 240: else 241: self.exec(Bio::FastaFormat.new(faa), parsing) 242: end 243: end