Class: Bio::SignalP::Result

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

Overview

The result of a SignalP program. Create using the output from -format short output and create_from_line()

Constant Summary collapse

@@nn_results = 
[:nn_Cmax, :nn_Cmax_position, :nn_Cmax_prediction, 
:nn_Ymax, :nn_Ymax_position, :nn_Ymax_prediction, 
:nn_Smax, :nn_Smax_position, :nn_Smax_prediction, 
:nn_Smean, :nn_Smean_prediction,
:nn_D, :nn_D_prediction]
@@hmm_results = 
[
:hmm_result, :hmm_Cmax, :hmm_Cmax_position, :hmm_Cmax_prediction, :hmm_Sprob, :hmm_Sprob_prediction]

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.all_result_names ⇒ Object

Return an array of symbols representing the names of the columns



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# File 'lib/bio/appl/signalp.rb', line 129

def self.all_result_names
  return [@@nn_results, @@hmm_results].flatten
end

.create_from_line(line) ⇒ Object

Create a new SignalpResult using a line from the signal p ‘short’ output format, version 3.0



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# File 'lib/bio/appl/signalp.rb', line 53

def self.create_from_line(line)
  # e.g.
  # # name                Cmax  pos ?  Ymax  pos ?  Smax  pos ?  Smean ?  D     ?   # name      !  Cmax  pos ?  Sprob ?
  # 526.m04658            0.734  19 Y  0.686  19 Y  0.933   6 Y  0.760 Y  0.723 Y 526.m04658  Q  0.037  19 N  0.004 N
  matches = line.split(/[ \t]+/)
  if matches.length != 21
    raise Exception, "Bad SignalP Short Line Found (#{matches.length}): '#{line}'"
  end
  
  i = 1
  result = Result.new
  result.nn_Cmax = matches[i].to_f; i += 1
  result.nn_Cmax_position = matches[i].to_i; i += 1
  result.nn_Cmax_prediction = to_bool matches[i]; i += 1
  result.nn_Ymax = matches[i].to_f; i += 1
  result.nn_Ymax_position = matches[i].to_i; i += 1
  result.nn_Ymax_prediction = to_bool matches[i]; i += 1
  result.nn_Smax = matches[i].to_f; i += 1
  result.nn_Smax_position = matches[i].to_i; i += 1
  result.nn_Smax_prediction = to_bool matches[i]; i += 1
  result.nn_Smean = matches[i].to_f; i += 1
  result.nn_Smean_prediction = to_bool matches[i]; i += 1
  result.nn_D = matches[i].to_f; i += 1
  result.nn_D_prediction = to_bool matches[i]; i += 1
  
  i+= 1
  result.hmm_result = matches[i]; i += 1
  result.hmm_Cmax = matches[i].to_f; i += 1
  result.hmm_Cmax_position = matches[i].to_i; i += 1
  result.hmm_Cmax_prediction = to_bool matches[i]; i += 1
  result.hmm_Sprob = matches[i].to_f; i += 1
  result.hmm_Sprob_prediction = to_bool matches[i]; i += 1
  
  return result
end

.to_bool(string) ⇒ Object 



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# File 'lib/bio/appl/signalp.rb', line 89

def self.to_bool(string)
  if string === 'Y'
    return true
  elsif string === 'N'
    return false
  else
    return nil
  end
end

Instance Method Details

#all_results ⇒ Object

Return an array of all the results. NN then HMM, as per SignalP short format



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# File 'lib/bio/appl/signalp.rb', line 114

def all_results
  all = []
  
  @@nn_results.each do |sym|
    all.push self.send(sym)
  end
  
  @@hmm_results.each do |sym|
    all.push self.send(sym)
  end
  
  return all
end

#classical_signal_sequence? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/appl/signalp.rb', line 105

def classical_signal_sequence?
  return @nn_D_prediction
end

#cleavage_site ⇒ Object

Return the number of the residue after the cleavage site ie. the first residue of the mature protein Taken from the Y score, as it was decided this is the best prediction



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# File 'lib/bio/appl/signalp.rb', line 136

def cleavage_site
  @nn_Ymax_position
end

#cleave(sequence) ⇒ Object

Given an amino acid sequence (as a string), chop it off and return the remnants



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# File 'lib/bio/appl/signalp.rb', line 142

def cleave(sequence)
  if signal?
    return sequence[cleavage_site-1..sequence.length-1]
  else
    return sequence
  end
end

#signal?(clazz = self) ⇒ Boolean

Does it have a signal peptide? It can be this class (default), or another class that responds to :nn_D_prediction and :hmm_Sprob_prediction

Returns:

  • (Boolean) 


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# File 'lib/bio/appl/signalp.rb', line 101

def signal?(clazz=self)
  return (clazz.send(:nn_D_prediction) or clazz.send(:hmm_Sprob_prediction))
end

#signal_anchor? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/appl/signalp.rb', line 109

def signal_anchor?
  return @hmm_Sprob_prediction
end