class Bio::PSORT::PSORT2
Bio::PSORT::PSORT2¶ ↑
Bio::PSORT::PSORT2 is a wapper class for the original PSORT program.
Example¶ ↑
serv = Bio::PSORT::PSORT2.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)
References¶ ↑
-
Nakai, K. and Horton, P., PSORT: a program for detecting the sorting signals of proteins and predicting their subcellular localization, Trends Biochem. Sci, 24(1) 34-35 (1999).
- PMID:10087920
Constants
Attributes
An accessor of the origin argument. Default setting is “yeast”.
An accessor of the title argument. Default setting is “QUERY”. The value is automatically setted if you use a query in Bio::FastaFormat.
Public Class Methods
Source
# File lib/bio/appl/psort.rb 331 def self.imsut 332 self.remote(ServerURI[:IMSUT][:PSORT2]) 333 end
Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote)
connecting to the IMSUT server.
Source
# File lib/bio/appl/psort.rb 357 def initialize(driver, origin = 'yeast') 358 @serv = driver 359 @origin = origin 360 @title = '' 361 end
Sets a server CGI Driver (Bio::PSORT::PSORT2::Remote).
Source
# File lib/bio/appl/psort.rb 337 def self.okazaki 338 self.remote(ServerURI[:Okazaki][:PSORT2]) 339 end
Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote) connecting to the NIBB server.
Source
# File lib/bio/appl/psort.rb 343 def self.peking 344 self.remote(ServerURI[:Peking][:PSORT2]) 345 end
Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote) connecting to the Peking server.
Source
# File lib/bio/appl/psort.rb 325 def self.remote(host, path = nil) 326 self.new(Remote.new(host, path)) 327 end
Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote).
PSORT official hosts:
key host path ------- ----------------------- -------------------- --------- IMSUT psort.ims.u-tokyo.ac.jp /cgi-bin/runpsort.pl (default) Okazaki psort.nibb.ac.jp /cgi-bin/runpsort.pl Peking srs.pku.edu.cn:8088 /cgi-bin/runpsort.pl
Public Instance Methods
Source
# File lib/bio/appl/psort.rb 367 def exec(faa, parsing = true) 368 if faa.class == Bio::FastaFormat 369 @title = faa.entry_id if @title == nil 370 @sequence = faa.seq 371 @serv.args = {'origin' => @origin, 'title' => @title} 372 @serv.parsing = parsing 373 return @serv.exec(@sequence) 374 else 375 self.exec(Bio::FastaFormat.new(faa), parsing) 376 end 377 end
Executes PSORT II prediction and returns Report object (Bio::PSORT::PSORT2::Report) if parsing = true. Returns PSORT II report in text if parsing = false.