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 ↑

Constants

FUNCTION

Organism specific parameter value: function names.

Attributes

output[R]

Output report.

Public Class Methods

new(func = 'METAZOA-specific') click to toggle source

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.

   # 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
new_with_fungi_function() click to toggle source

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

   # File lib/bio/appl/pts1.rb
74 def self.new_with_fungi_function
75   self.new('FUNGI-specific')
76 end
new_with_general_function() click to toggle source

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

   # File lib/bio/appl/pts1.rb
79 def self.new_with_general_function
80   self.new('GENERAL')
81 end
new_with_metazoa_function() click to toggle source

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

   # File lib/bio/appl/pts1.rb
69 def self.new_with_metazoa_function
70   self.new('METAZOA-specific')
71 end

Public Instance Methods

exec(query) click to toggle source

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"))

    # 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
function(func = nil) click to toggle source

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"

    # 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