class Bio::PSORT::PSORT2

Bio::PSORT::PSORT2

Bio::PSORT::PSORT2 is a wapper class for the original PSORT program.

Example

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)

References

  1. 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).

    PMID:10087920

Constants

Features

Feature name codes

FeaturesLong

Feature name codes (long version).

SclNames

Subcellular localization name codes used by PSORT2

Attributes

origin[RW]

An accessor of the origin argument. Default setting is “yeast''.

title[RW]

An accessor of the title argument. Default setting is “QUERY''. The value is automatically setted if you use a query in Bio::FastaFormat.

Public Class Methods

imsut() click to toggle source

Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote)

connecting to the IMSUT server.

    # File lib/bio/appl/psort.rb
331 def self.imsut
332   self.remote(ServerURI[:IMSUT][:PSORT2])
333 end
new(driver, origin = 'yeast') click to toggle source

Sets a server CGI Driver (Bio::PSORT::PSORT2::Remote).

    # File lib/bio/appl/psort.rb
357 def initialize(driver, origin = 'yeast')
358   @serv   = driver
359   @origin = origin
360   @title  = ''
361 end
okazaki() click to toggle source

Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote) connecting to the NIBB server.

    # File lib/bio/appl/psort.rb
337 def self.okazaki
338   self.remote(ServerURI[:Okazaki][:PSORT2])
339 end
peking() click to toggle source

Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote) connecting to the Peking server.

    # File lib/bio/appl/psort.rb
343 def self.peking
344   self.remote(ServerURI[:Peking][:PSORT2])
345 end
remote(host, path = nil) click to toggle source

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
325 def self.remote(host, path = nil)
326   self.new(Remote.new(host, path))
327 end

Public Instance Methods

exec(faa, parsing = true) click to toggle source

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
367 def exec(faa, parsing = true)
368   if faa.class == Bio::FastaFormat
369     @title = faa.entry_id if @title == nil
370     @sequence = faa.seq
371     @serv.args = {'origin' => @origin, 'title' => @title}
372     @serv.parsing = parsing
373     return @serv.exec(@sequence)
374   else
375     self.exec(Bio::FastaFormat.new(faa), parsing)
376   end
377 end