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)
Nakai, K. and Kanehisa, M., A knowledge base for predicting protein localization sites in eukaryotic cells, Genomics 14, 897-911 (1992).
An accessor of the origin argument. Default setting is "yeast". Usable values:
Gram-positive bacterium
Gram-negative bacterium
yeast
animal
plant
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 def self.imsut self.new(Remote.new(ServerURI[:IMSUT][:PSORT1])) end
Sets a cgi client (Bio::PSORT::PSORT1::Remote).
# File lib/bio/appl/psort.rb, line 199 def initialize(driver, origin = 'yeast', title = 'MYSEQ') @serv = driver @origin = origin # Gram-positive bacterium, Gram-negative bacterium, # yeast, aminal, plant @title = title @sequence = '' end
Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote) connecting to the NIBB server.
# File lib/bio/appl/psort.rb, line 185 def self.okazaki self.new(Remote.new(ServerURI[:Okazaki][:PSORT1])) end
Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote) connecting to the Peking server.
# File lib/bio/appl/psort.rb, line 192 def self.peking self.new(Remote.new(ServerURI[:Peking][:PSORT1])) 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 def exec(faa, parsing = true) if faa.class == Bio::FastaFormat @title = faa.entry_id if @title == 'MYSEQ' @sequence = faa.seq @serv.args = {'title' => @title, 'origin' => @origin} @serv.parsing = parsing return @serv.exec(sequence) else self.exec(Bio::FastaFormat.new(faa), parsing) end end
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