class Bio::PTS1::Report

Parser for the PTS1 prediction Report (in HTML).

Attributes

cterm[R]

Amino acids subsequence at C-terminal region.

entry_id[R]

Query sequence name.

fp[R]

False positive probability

output[R]

Raw output

prediction[R]

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

profile[R]

Profile

score[R]

Score

sppta[R]

S_ppt (accessibility)

spptna[R]

S_ppt (non accessibility)

Public Class Methods

new(str) click to toggle source

Parsing PTS1 HTML report.

Example

report = Bio::PTS1::Report.new(str)
report.cterm
    # File lib/bio/appl/pts1.rb
205 def initialize(str)
206   @cterm   = ''
207   @score   = 0
208   @profile = 0
209   @spptna  = 0
210   @sppta   = 0
211   @fp      = 0
212   @prediction = 0
213   
214   if /PTS1 query prediction/m =~ str
215     @output = str
216     parse
217   else
218     raise 
219   end
220 end

Private Instance Methods

parse() click to toggle source
    # File lib/bio/appl/pts1.rb
225 def parse
226   @output.each_line do |line|
227     case line
228     when /Name<\/td><td>(\S.+)<\/td><\/tr>/
229       @entry_id = $1
230     when /C-terminus<\/td><td>(\w+)<\/td>/
231       @cterm = $1
232     when /Score<\/b><td><b>(-?\d.+?)<\/b><\/td><\/tr>/
233       @score = $1
234     when /Profile<\/i><\/td><td>(.+?)<\/td>/
235       @profile = $1
236     when /S_ppt \(non-accessibility\)<\/i><\/td><td>(.+?)<\/td>/
237       @spptna = $1
238     when /S_ppt \(accessibility\)<\/i><\/td><td>(.+?)<\/td>/
239       @sppta = $1
240     when /P\(false positive\)<\/i><\/td><td>(.+?)<\/td>/
241       @fp = $1
242     when /Prediction classification<\/i><\/td><td>(\w.+?)<\/td>/
243       @prediction = $1
244     else
245     end
246   end
247 end