class Bio::SignalP::Version3::Result
The result of a SignalP
program. Create using the output from -format short output and create_from_line
()
Public Class Methods
all_result_names()
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Return an array of symbols representing the names of the columns
# File lib/bio/appl/signalp3.rb, line 97 def self.all_result_names return [@@nn_results, @@hmm_results].flatten end
create_from_line(line)
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Create a new SignalpResult using a line from the signal p ‘short’ output format, version 3.0
# 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
Public Instance Methods
all_results()
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Return an array of all the results. NN then HMM, as per SignalP
short format
# 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?()
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# File lib/bio/appl/signalp3.rb, line 73 def classical_signal_sequence? return @nn_D_prediction end
cleavage_site()
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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/signalp3.rb, line 104 def cleavage_site @nn_Ymax_position end
signal?(clazz=self)
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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/signalp3.rb, line 69 def signal?(clazz=self) return (clazz.send(:nn_D_prediction) or clazz.send(:hmm_Sprob_prediction)) end
signal_anchor?()
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# File lib/bio/appl/signalp3.rb, line 77 def signal_anchor? return @hmm_Sprob_prediction end