Bio::PTS1 - A web service client class for PTS1 predictor.

Peroxisomal targeting signal type 1 (PTS1) predictor

Bio::PTS1 class is a client of the PTS1 predictor.

Examples

  require 'bio'
  sp = Bio::SPTR.new(Bio::Fetch.query("sp", "p53_human"))
  faa = sp.seq.to_fasta(sp.entry_id)
  pts1 = Bio::PTS1.new
  report = pts1.exec_remote(faa)
  report.output     #=> "<HTML>\n<HEAD><TITLE>PTS1 Prediction Server ..."
  report.prediction #=> "Not targeted"
  report.cterm      #=> "KLMFKTEGPDSD"
  report.score      #=> "-79.881"
  report.fp         #=> "67.79%"
  report.sppta      #=> "-1.110"
  report.spptna     #=> "-41.937"
  report.profile    #=> "-36.834"

References

The PTS1 predictor mendel.imp.ac.at/mendeljsp/sat/pts1/PTS1predictor.jsp
Neuberger G, Maurer-Stroh S, Eisenhaber B, Hartig A, Eisenhaber F. Motif refinement of the peroxisomal targeting signal 1 and evaluation of taxon-specific differences. J Mol Biol. 2003 May 2;328(3):567-79. PMID: 12706717
Neuberger G, Maurer-Stroh S, Eisenhaber B, Hartig A, Eisenhaber F. Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence. J Mol Biol. 2003 May 2;328(3):581-92. PMID: 12706718

Methods

exec function new new_with_fungi_function new_with_general_function new_with_metazoa_function

Classes and Modules

Class Bio::PTS1::Report

Constants

FUNCTION = { 'METAZOA-specific' => 1, 'FUNGI-specific' => 2, 'GENERAL' => 3, } Organism specific parameter value: function names.

Attributes

function	[R]	Used function name (Integer). function_name = Bio::PTS1::FUNCTION.find_all {\|k,v\| v == pts1.function }[0][0]
output	[R]	Output report.

Public Class methods

new(func = 'METAZOA-specific')

Constructs Bio::PTS1 web service client.

Examples

  serv_default_metazoa_specific = Bio::PTS1.new
  serv_general_function = Bio::PTS1.new('GENERAL')
  serv_fungi_specific = Bio::PTS1.new(2)    # See Bio::PTS1::FUNCTION.

[Source]

     # File lib/bio/appl/pts1.rb, line 96
 96:   def initialize(func = 'METAZOA-specific')
 97:     @host = "mendel.imp.ac.at"
 98:     @cgi_path = "/sat/pts1/cgi-bin/pts1.cgi"
 99:     @output = nil
100:     @function = function(func)
101:   end

new_with_fungi_function()

Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION[‘FUNGI-specific’])

[Source]

    # File lib/bio/appl/pts1.rb, line 78
78:   def self.new_with_fungi_function
79:     self.new('FUNGI-specific')
80:   end

new_with_general_function()

Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION[‘GENERAL’])

[Source]

    # File lib/bio/appl/pts1.rb, line 83
83:   def self.new_with_general_function
84:     self.new('GENERAL')
85:   end

new_with_metazoa_function()

Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION[‘METAZOA-specific’])

[Source]

    # File lib/bio/appl/pts1.rb, line 73
73:   def self.new_with_metazoa_function
74:     self.new('METAZOA-specific')
75:   end

Public Instance methods

exec(query)

Executes the query request and returns result output in Bio::PTS1::Report. The query argument is available both aSting in fasta format text and aBio::FastaFormat.

Examples

  require 'bio'
  pts1 = Bio::PTS1.new
  pts1.exec(">title\nKLMFKTEGPDSD")

  pts1.exec(Bio::FastaFormat.new(">title\nKLMFKTEGPDSD"))

[Source]

     # File lib/bio/appl/pts1.rb, line 146
146:   def exec(query)
147:     seq = set_sequence_in_fastaformat(query)
148:     
149:     @form_data = {'function' => @function.values.join(''),
150:                   'sequence' => seq.seq,
151:                   'name'     => seq.definition }
152:     @uri = URI.parse(["http:/", @host, @cgi_path].join('/'))
153: 
154:     result = Bio::Command.post_form(@uri, @form_data)
155:     @output = Report.new(result.body)
156:     
157:     return @output
158:   end

function(func = nil)

Sets and shows the function parameter.

Organism specific parameter: function names (Bio::PTS1::FUNTION.keys).

Examples

 # sets function name parameter.
 serv = Bio::PTS1.new
 serv.function('METAZOA-specific')

 # shows function name parameter.
 serv.function #=> "METAZOA-specific"

[Source]

     # File lib/bio/appl/pts1.rb, line 118
118:   def function(func = nil)
119:     return @function.keys.join('') if func == nil
120: 
121:     if FUNCTION.values.include?(func)
122:       @function = Hash[*FUNCTION.find {|x| x[1] == func}]
123:     elsif FUNCTION[func]
124:       @function = {func => FUNCTION[func]} 
125:     else
126:       raise ArgumentError, 
127:             "Invalid argument: #{func}", 
128:             "Available function names: #{FUNCTION.keys.inspect}"
129:     end
130:     @function
131:   end