class Bio::PTS1
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¶ ↑
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The
PTS1predictor 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
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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
Constants
- FUNCTION
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Organism specific parameter value: function names.
Attributes
Output report.
Public Class Methods
Source
# File lib/bio/appl/pts1.rb 92 def initialize(func = 'METAZOA-specific') 93 @uri = "https://mendel.imp.ac.at/jspcgi/cgi-bin/pts1/pts1.cgi" 94 @output = nil 95 @function = function(func) 96 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.
Source
# File lib/bio/appl/pts1.rb 74 def self.new_with_fungi_function 75 self.new('FUNGI-specific') 76 end
Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION['FUNGI-specific'])
Source
# File lib/bio/appl/pts1.rb 79 def self.new_with_general_function 80 self.new('GENERAL') 81 end
Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION['GENERAL'])
Source
# File lib/bio/appl/pts1.rb 69 def self.new_with_metazoa_function 70 self.new('METAZOA-specific') 71 end
Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION['METAZOA-specific'])
Public Instance Methods
Source
# File lib/bio/appl/pts1.rb 141 def exec(query) 142 seq = set_sequence_in_fastaformat(query) 143 144 @form_data = {'function' => @function.values.join(''), 145 'sequence' => seq.seq, 146 'name' => seq.definition } 147 148 result = Bio::Command.post_form(@uri, @form_data) 149 @output = Report.new(result.body) 150 151 return @output 152 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"))
Source
# File lib/bio/appl/pts1.rb 113 def function(func = nil) 114 return @function.keys.join('') if func == nil 115 116 if FUNCTION.values.include?(func) 117 @function = Hash[*FUNCTION.find {|x| x[1] == func}] 118 elsif FUNCTION[func] 119 @function = {func => FUNCTION[func]} 120 else 121 raise ArgumentError, 122 "Invalid argument: #{func}", 123 "Available function names: #{FUNCTION.keys.inspect}" 124 end 125 @function 126 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"