class Bio::PSORT::PSORT1
Bio::PSORT::PSORT1¶ ↑
Bio::PSORT::PSORT1 is a wapper class for the original PSORT program.
Example¶ ↑
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)
References¶ ↑
-
Nakai, K. and Kanehisa, M., A knowledge base for predicting protein localization sites in eukaryotic cells, Genomics 14, 897-911 (1992).
- PMID:1478671
Attributes
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 query sequence argument.
An accessor of the title argument. Default setting is ‘MYSEQ’. The value is automatically setted if you use a query in Bio::FastaFormat.
Public Class Methods
Source
# File lib/bio/appl/psort.rb 178 def self.imsut 179 self.new(Remote.new(ServerURI[:IMSUT][:PSORT1])) 180 end
Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote)
connecting to the IMSUT server.
Source
# File lib/bio/appl/psort.rb 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
Sets a cgi client (Bio::PSORT::PSORT1::Remote).
Source
# File lib/bio/appl/psort.rb 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 NIBB server.
Source
# File lib/bio/appl/psort.rb 192 def self.peking 193 self.new(Remote.new(ServerURI[:Peking][:PSORT1])) 194 end
Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote) connecting to the Peking server.
Public Instance Methods
Source
# File lib/bio/appl/psort.rb 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
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.