Bio::PSORT::PSORT1::Report

    # File lib/bio/appl/psort/report.rb, line 36
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, line 72
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, line 31
31:         def self.parser(output_report)
32:           self.default_parser(output_report)
33:         end