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
Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote)
connecting to the IMSUT server.
# File lib/bio/appl/psort.rb, line 331 def self.imsut self.remote(ServerURI[:IMSUT][:PSORT2]) end
Sets a server CGI Driver (Bio::PSORT::PSORT2::Remote).
# File lib/bio/appl/psort.rb, line 357 def initialize(driver, origin = 'yeast') @serv = driver @origin = origin @title = '' end
Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote) connecting to the NIBB server.
# File lib/bio/appl/psort.rb, line 337 def self.okazaki self.remote(ServerURI[:Okazaki][:PSORT2]) end
Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote) connecting to the Peking server.
# File lib/bio/appl/psort.rb, line 343 def self.peking self.remote(ServerURI[:Peking][:PSORT2]) 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
# File lib/bio/appl/psort.rb, line 325 def self.remote(host, path = nil) self.new(Remote.new(host, path)) end
Public Instance Methods
Executes PSORT II prediction and returns Report object (Bio::PSORT::PSORT2::Report) if parsing = true. Returns PSORT II report in text if parsing = false.
# File lib/bio/appl/psort.rb, line 367 def exec(faa, parsing = true) if faa.class == Bio::FastaFormat @title = faa.entry_id if @title == nil @sequence = faa.seq @serv.args = {'origin' => @origin, 'title' => @title} @serv.parsing = parsing return @serv.exec(@sequence) else self.exec(Bio::FastaFormat.new(faa), parsing) end end