Class | Bio::PTS1 |
In: |
lib/bio/appl/pts1.rb
|
Parent: | Object |
Bio::PTS1 class is a client of the PTS1 predictor.
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"
FUNCTION | = | { 'METAZOA-specific' => 1, 'FUNGI-specific' => 2, 'GENERAL' => 3, } | Organism specific parameter value: function names. |
output | [R] | Output report. |
Constructs Bio::PTS1 web service client.
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.
# File lib/bio/appl/pts1.rb, line 92 92: def initialize(func = 'METAZOA-specific') 93: @uri = "http://mendel.imp.ac.at/jspcgi/cgi-bin/pts1/pts1.cgi" 94: @output = nil 95: @function = function(func) 96: end
Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION[‘FUNGI-specific’])
# File lib/bio/appl/pts1.rb, line 74 74: def self.new_with_fungi_function 75: self.new('FUNGI-specific') 76: end
Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION[‘GENERAL’])
# File lib/bio/appl/pts1.rb, line 79 79: def self.new_with_general_function 80: self.new('GENERAL') 81: end
Short-cut for Bio::PTS1.new(Bio::PTS1::FUNCTION[‘METAZOA-specific’])
# File lib/bio/appl/pts1.rb, line 69 69: def self.new_with_metazoa_function 70: self.new('METAZOA-specific') 71: 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.
require 'bio' pts1 = Bio::PTS1.new pts1.exec(">title\nKLMFKTEGPDSD") pts1.exec(Bio::FastaFormat.new(">title\nKLMFKTEGPDSD"))
# File lib/bio/appl/pts1.rb, line 141 141: 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
Sets and shows the function parameter.
Organism specific parameter: function names (Bio::PTS1::FUNTION.keys).
# sets function name parameter. serv = Bio::PTS1.new serv.function('METAZOA-specific') # shows function name parameter. serv.function #=> "METAZOA-specific"
# File lib/bio/appl/pts1.rb, line 113 113: 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