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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 <n@bioruby.org>
# 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 #=> "<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
# 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
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