Class: Bio::PTS1::Report

Inherits:
Object show all
Defined in:
lib/bio/appl/pts1.rb

Overview

Parser for the PTS1 prediction Report (in HTML).

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(str) ⇒ Report

Parsing PTS1 HTML report.

Example

report = Bio::PTS1::Report.new(str)
report.cterm

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# File 'lib/bio/appl/pts1.rb', line 205

def initialize(str)
  @cterm   = ''
  @score   = 0
  @profile = 0
  @spptna  = 0
  @sppta   = 0
  @fp      = 0
  @prediction = 0
  
  if /PTS1 query prediction/m =~ str
    @output = str
    parse
  else
    raise 
  end
end

Instance Attribute Details

#ctermObject (readonly)

Amino acids subsequence at C-terminal region.


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# File 'lib/bio/appl/pts1.rb', line 175

def cterm
  @cterm
end

#entry_idObject (readonly)

Query sequence name.


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# File 'lib/bio/appl/pts1.rb', line 172

def entry_id
  @entry_id
end

#fpObject (readonly)

False positive probability


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# File 'lib/bio/appl/pts1.rb', line 190

def fp
  @fp
end

#outputObject (readonly)

Raw output


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# File 'lib/bio/appl/pts1.rb', line 196

def output
  @output
end

#predictionObject (readonly)

Prediction (“Targeted”, “Twilight zone” and “Not targeted”)


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# File 'lib/bio/appl/pts1.rb', line 193

def prediction
  @prediction
end

#profileObject (readonly)

Profile


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# File 'lib/bio/appl/pts1.rb', line 181

def profile
  @profile
end

#scoreObject (readonly)

Score


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# File 'lib/bio/appl/pts1.rb', line 178

def score
  @score
end

#spptaObject (readonly)

S_ppt (accessibility)


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# File 'lib/bio/appl/pts1.rb', line 187

def sppta
  @sppta
end

#spptnaObject (readonly)

S_ppt (non accessibility)


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# File 'lib/bio/appl/pts1.rb', line 184

def spptna
  @spptna
end