Bio::PSORT::PSORT2 is a wapper class for the original PSORT program.
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)
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).
An accessor of the title argument. Default setting is "QUERY". The value is automatically setted if you use a query in Bio::FastaFormat.
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
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
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