class Bio::SignalP::Version4::Result

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

Constants

Cmax
Cmax_position
D
Dmaxcut
Smax
Smax_position
Smean
Ymax
Ymax_position

Public Class Methods

create_from_line(line) click to toggle source

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

# File lib/bio/appl/signalp4.rb, line 29
def self.create_from_line(line)
  # e.g.
  #$ ~/bioinfo/signalp-4.0/signalp /tmp/acp
  ## SignalP-4.0 euk predictions
  ## name                     Cmax  pos  Ymax  pos  Smax  pos  Smean   D     ?  Dmaxcut    Networks-used
  #acp                        0.871  17  0.863  17  0.886   1  0.844   0.853 Y  0.450      SignalP-noTM
  matches = line.split(/[ \t]+/)
  if matches.length != Bio::SignalP::NUM_FIELDS_IN_VERSION4_SHORT_OUTPUT
    raise Exception, "Bad SignalP Short Line Found (#{matches.length}): '#{line}'"
  end
  
  i = 1
  result = Result.new
  result.Cmax = matches[i].to_f; i += 1
  result.Cmax_position = matches[i].to_i; i += 1
  result.Ymax = matches[i].to_f; i += 1
  result.Ymax_position = matches[i].to_i; i += 1
  result.Smax = matches[i].to_f; i += 1
  result.Smax_position = matches[i].to_i; i += 1
  result.Smean = matches[i].to_f; i += 1
  result.D = matches[i].to_f; i += 1
  result.prediction = result.to_bool matches[i]; i += 1
  result.Dmaxcut = matches[i].to_f; i += 1
  result.networks_used = matches[i]; i += 1
  
  return result
end

Public Instance Methods

cleavage_site() click to toggle source

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

# File lib/bio/appl/signalp4.rb, line 66
def cleavage_site
  @Ymax_position
end
signal?(clazz=self) click to toggle source

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

# File lib/bio/appl/signalp4.rb, line 59
def signal?(clazz=self)
  return clazz.send(:prediction)
end