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]

Methods

exec imsut new okazaki peking

Classes and Modules

Class Bio::PSORT::PSORT1::Remote
Class Bio::PSORT::PSORT1::Report

Attributes

origin	[RW]	An accessor of the origin argument. Default setting is "yeast". Usable values: Gram-positive bacterium Gram-negative bacterium yeast animal plant
sequence	[RW]	An accessor of the query sequence argument.
title	[RW]	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

imsut()

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

[Source]

     # File lib/bio/appl/psort.rb, line 178
178:       def self.imsut
179:         self.new(Remote.new(ServerURI[:IMSUT][:PSORT1]))
180:       end

new(driver, origin = 'yeast', title = 'MYSEQ')

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

[Source]

     # File lib/bio/appl/psort.rb, line 199
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

okazaki()

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

[Source]

     # File lib/bio/appl/psort.rb, line 185
185:       def self.okazaki
186:         self.new(Remote.new(ServerURI[:Okazaki][:PSORT1]))
187:       end

peking()

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

[Source]

     # File lib/bio/appl/psort.rb, line 192
192:       def self.peking
193:         self.new(Remote.new(ServerURI[:Peking][:PSORT1]))
194:       end

Public Instance methods

exec(faa, parsing = true)

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.

[Source]

     # File lib/bio/appl/psort.rb, line 233
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