module Bio # # = bio/appl/pts1.rb - A web service client of PTS1, predicting for the # peroxisomal targeting signal type 1. # # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao # License:: The Ruby License # # $Id:$ # require 'uri' require 'net/http' require 'bio/db/fasta' require 'bio/command' # = 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 #=> "\nPTS1 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 # http://mendel.imp.ac.at/pts1/ # # * 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 # class PTS1 # Organism specific parameter value: function names. FUNCTION = { 'METAZOA-specific' => 1, 'FUNGI-specific' => 2, 'GENERAL' => 3, } # Output report. attr_reader :output # Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION['METAZOA-specific']) def self.new_with_metazoa_function self.new('METAZOA-specific') end # Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION['FUNGI-specific']) def self.new_with_fungi_function self.new('FUNGI-specific') end # Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION['GENERAL']) def self.new_with_general_function self.new('GENERAL') end # 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. # def initialize(func = 'METAZOA-specific') @uri = "http://mendel.imp.ac.at/jspcgi/cgi-bin/pts1/pts1.cgi" @output = nil @function = function(func) end # 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" # def function(func = nil) return @function.keys.join('') if func == nil if FUNCTION.values.include?(func) @function = Hash[*FUNCTION.find {|x| x[1] == func}] elsif FUNCTION[func] @function = {func => FUNCTION[func]} else raise ArgumentError, "Invalid argument: #{func}", "Available function names: #{FUNCTION.keys.inspect}" end @function end # 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")) # def exec(query) seq = set_sequence_in_fastaformat(query) @form_data = {'function' => @function.values.join(''), 'sequence' => seq.seq, 'name' => seq.definition } result = Bio::Command.post_form(@uri, @form_data) @output = Report.new(result.body) return @output end private # Sets query sequence in Fasta Format if any. def set_sequence_in_fastaformat(query) if query.class == Bio::FastaFormat return query else return Bio::FastaFormat.new(query) end end # = Parser for the PTS1 prediction Report (in HTML). # # class Report # Query sequence name. attr_reader :entry_id # Amino acids subsequence at C-terminal region. attr_reader :cterm # Score attr_reader :score # Profile attr_reader :profile # S_ppt (non accessibility) attr_reader :spptna # S_ppt (accessibility) attr_reader :sppta # False positive probability attr_reader :fp # Prediction ("Targeted", "Twilight zone" and "Not targeted") attr_reader :prediction # Raw output attr_reader :output # Parsing PTS1 HTML report. # # == Example # # report = Bio::PTS1::Report.new(str) # report.cterm # def initialize(str) @cterm = '' @score = 0 @profile = 0 @spptna = 0 @sppta = 0 @fp = 0 @prediction = 0 if /PTS1 query prediction/m =~ str @output = str parse else raise end end private def parse @output.each_line do |line| case line when /Name<\/td><td>(\S.+)<\/td><\/tr>/ @entry_id = $1 when /C-terminus<\/td><td>(\w+)<\/td>/ @cterm = $1 when /Score<\/b><td><b>(-?\d.+?)<\/b><\/td><\/tr>/ @score = $1 when /Profile<\/i><\/td><td>(.+?)<\/td>/ @profile = $1 when /S_ppt \(non-accessibility\)<\/i><\/td><td>(.+?)<\/td>/ @spptna = $1 when /S_ppt \(accessibility\)<\/i><\/td><td>(.+?)<\/td>/ @sppta = $1 when /P\(false positive\)<\/i><\/td><td>(.+?)<\/td>/ @fp = $1 when /Prediction classification<\/i><\/td><td>(\w.+?)<\/td>/ @prediction = $1 else end end end end # class Report end # class PTS1 end # module Bio