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

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

    PMID:1478671

Attributes

origin[RW]

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

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() click to toggle source

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

connecting to the IMSUT server.

# File lib/bio/appl/psort.rb, line 178
def self.imsut
  self.new(Remote.new(ServerURI[:IMSUT][:PSORT1]))
end
new(driver, origin = 'yeast', title = 'MYSEQ') click to toggle source

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

# 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
okazaki() click to toggle source

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

# File lib/bio/appl/psort.rb, line 185
def self.okazaki
  self.new(Remote.new(ServerURI[:Okazaki][:PSORT1]))
end
peking() click to toggle source

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

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

Public Instance Methods

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

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.

# 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