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, line 331
def self.imsut
  self.remote(ServerURI[:IMSUT][:PSORT2])
end
new(driver, origin = 'yeast') click to toggle source

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

# File lib/bio/appl/psort.rb, line 357
def initialize(driver, origin = 'yeast')
  @serv   = driver
  @origin = origin
  @title  = ''
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, line 337
def self.okazaki
  self.remote(ServerURI[:Okazaki][:PSORT2])
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, line 343
def self.peking
  self.remote(ServerURI[:Peking][:PSORT2])
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, line 325
def self.remote(host, path = nil)
  self.new(Remote.new(host, path))
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, line 367
def exec(faa, parsing = true)
  if faa.class == Bio::FastaFormat
    @title = faa.entry_id if @title == nil
    @sequence = faa.seq
    @serv.args = {'origin' => @origin, 'title' => @title}
    @serv.parsing = parsing
    return @serv.exec(@sequence)
  else
    self.exec(Bio::FastaFormat.new(faa), parsing)
  end
end