Class: Bio::PlasmoAP

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/plasmoap.rb

Overview

PlasmoAP is a program for predicting apicoplast targetting sequences in Plasmodium falciparum (the most fatal causative agent of malaria). This algorithm was designed based on what was outlined in the PlasmoAP journal article

Dissecting apicoplast targeting in the malaria parasite Plasmodium falciparum. Foth BJ, Ralph SA, Tonkin CJ, Struck NS, Fraunholz M, Roos DS, Cowman AF, McFadden GI. Science. 2003 Jan 31;299(5607):705-8. PMID: 12560551

Instance Method Summary collapse

Instance Method Details

#calculate_score(sequence, has_signal_sequence = nil, signalp_cleaved_sequence = nil) ⇒ Object

Calculate the PlasmoAP score for a sequence (a string of amino acids) sequence - the amino acids to test on has_signal_sequence - Define if it has a signal sequence or not. The default nil specifies that it should be worked out by SignalP.



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# File 'lib/bio/appl/plasmoap.rb', line 21

def calculate_score(sequence, has_signal_sequence = nil, signalp_cleaved_sequence = nil)
  # Only calculate signal sequence if it isn't already set by the parameter
  if has_signal_sequence.nil?
    # to_s means the sequence can be amino acid string or proper Bio::Sequence::AA object
    signalp = Bio::SignalP::Wrapper.new.calculate(sequence.to_s)
    has_signal_sequence = signalp.classical_signal_sequence?
    
    signalp_cleaved_sequence = signalp.cleave(sequence)
  elsif signalp_cleaved_sequence.nil?
    raise ArgumentError, "if the has_signal_sequence parameter is defined, then so must the signalp_cleaved_sequence be as well"
  end
  
  return PlasmoAPResult.new(0) if !has_signal_sequence #Both set of rules need a signal peptide
  
  cleaved = Bio::Sequence::AA.new(signalp_cleaved_sequence)
  
  set1 = set1?(cleaved)
  set2 = set2?(cleaved)
  additional = additional?(cleaved)
  
  points = 0
  points += 2 if set1
  points += 2 if set2
  points += 1 if additional
  return PlasmoAPResult.new(points)
end