# File lib/bio/appl/psort/report.rb
36 def self.default_parser(output_report)
37   rpt = self.new
38   rpt.raw = output_report
39   query_info = output_report.scan(/^Query Information\n\n(.+?)\n\n/m)[0][0].split(/\n/)
40   result_info = output_report.scan(/^Result Information\n\n(.+?)\n\n\*/m)[0][0]
41   step1 = output_report.scan(/^\*\*\* Reasoning Step: 1\n\n(.+?)\n\n/m)[0][0]
42   step2 = output_report.scan(/^\*\*\* Reasoning Step: 2\n\n(.+?)\n\n/m)[0][0]
43   final_result = output_report.scan(/\n\n----- Final Results -----\n\n(.+?)\n\n\n/m)[0][0]
44 
45   rpt.entry_id = query_info[2].scan(/^>(\S+) */).to_s
46   rpt.origin   = query_info[0].scan(/ORIGIN (\w+)/).to_s
47   rpt.sequence = Bio::Sequence::AA.new(query_info[3..query_info.size].to_s)
48   # rpt.reasoning
49 
50   rpt.final_result = final_result.split(/\n/).map {|x|
51     x = x.strip.split(/---/).map {|y| y.strip }
52     { 'prediction' => x[0], 
53       'certainty'  => x[1].scan(/Certainty= (\d\.\d{3})/).to_s,
54       'comment'    => x[1].scan(/\((\w+)\)/).to_s
55     }
56   }
57   return rpt
58 end

   # File lib/bio/appl/psort/report.rb
72 def initialize(entry_id = '', origin = '', title = '', sequence = '',
73                result_info = '', reasoning = {}, final_result = [])
74   @entry_id = entry_id
75   @origin = origin
76   @title = title
77   @sequence = sequence
78   @result_info = result_info
79   @reasoning = reasoning
80   @final_result = final_result
81   @raw = ''
82 end

   # File lib/bio/appl/psort/report.rb
31 def self.parser(output_report)
32   self.default_parser(output_report)
33 end