Class: Bio::PSORT::PSORT1

Inherits:
Object show all
Defined in:
lib/bio/appl/psort.rb,
lib/bio/appl/psort/report.rb

Overview

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

  1. Nakai, K. and Kanehisa, M., A knowledge base for predicting protein localization sites in eukaryotic cells, Genomics 14, 897-911 (1992).

    PMID:1478671

Defined Under Namespace

Classes: Remote, Report

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(driver, origin = 'yeast', title = 'MYSEQ') ⇒ PSORT1

Sets a cgi client (Bio::PSORT::PSORT1::Remote).



199
200
201
202
203
204
205
 
# 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

Instance Attribute Details

#origin ⇒ Object

An accessor of the origin argument. Default setting is “yeast”. Usable values:

  1. Gram-positive bacterium

  2. Gram-negative bacterium

  3. yeast

  4. animal

  5. plant



215
216
217
 
# File 'lib/bio/appl/psort.rb', line 215

def origin
  @origin
end

#sequence ⇒ Object

An accessor of the query sequence argument.



218
219
220
 
# File 'lib/bio/appl/psort.rb', line 218

def sequence
  @sequence
end

#title ⇒ Object

An accessor of the title argument. Default setting is ‘MYSEQ’. The value is automatically setted if you use a query in Bio::FastaFormat.



223
224
225
 
# File 'lib/bio/appl/psort.rb', line 223

def title
  @title
end

Class Method Details

.imsut ⇒ Object

Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote)

connecting to the IMSUT server.



178
179
180
 
# File 'lib/bio/appl/psort.rb', line 178

def self.imsut
  self.new(Remote.new(ServerURI[:IMSUT][:PSORT1]))
end

.okazaki ⇒ Object

Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote) connecting to the NIBB server.



185
186
187
 
# File 'lib/bio/appl/psort.rb', line 185

def self.okazaki
  self.new(Remote.new(ServerURI[:Okazaki][:PSORT1]))
end

.peking ⇒ Object

Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote) connecting to the Peking server.



192
193
194
 
# File 'lib/bio/appl/psort.rb', line 192

def self.peking
  self.new(Remote.new(ServerURI[:Peking][:PSORT1]))
end

Instance Method Details

#exec(faa, parsing = true) ⇒ Object

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.



233
234
235
236
237
238
239
240
241
242
243
 
# 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