Class: Bio::SignalP::Version3::Result

Inherits:
Object
  • Object
show all
Includes:
Common
Defined in:
lib/bio/appl/signalp3.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

Methods included from Common

#cleave, #to_bool

Class Method Details

.all_result_names ⇒ Object

Return an array of symbols representing the names of the columns



97
98
99
 
# File 'lib/bio/appl/signalp3.rb', line 97

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



31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
 
# File 'lib/bio/appl/signalp3.rb', line 31

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 != Bio::SignalP::NUM_FIELDS_IN_VERSION3_SHORT_OUTPUT
    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 = result.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 = result.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 = result.to_bool matches[i]; i += 1
  result.nn_Smean = matches[i].to_f; i += 1
  result.nn_Smean_prediction = result.to_bool matches[i]; i += 1
  result.nn_D = matches[i].to_f; i += 1
  result.nn_D_prediction = result.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 = result.to_bool matches[i]; i += 1
  result.hmm_Sprob = matches[i].to_f; i += 1
  result.hmm_Sprob_prediction = result.to_bool matches[i]; i += 1
  
  return result
end

Instance Method Details

#all_results ⇒ Object

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



82
83
84
85
86
87
88
89
90
91
92
93
94
 
# File 'lib/bio/appl/signalp3.rb', line 82

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) 


73
74
75
 
# File 'lib/bio/appl/signalp3.rb', line 73

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



104
105
106
 
# File 'lib/bio/appl/signalp3.rb', line 104

def cleavage_site
  @nn_Ymax_position
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) 


69
70
71
 
# File 'lib/bio/appl/signalp3.rb', line 69

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

#signal_anchor? ⇒ Boolean

Returns:

  • (Boolean) 


77
78
79
 
# File 'lib/bio/appl/signalp3.rb', line 77

def signal_anchor?
  return @hmm_Sprob_prediction
end