Class | Bio::PSORT::PSORT1::Report |
In: |
lib/bio/appl/psort/report.rb
|
Parent: | Object |
entry_id | [RW] | |
final_result | [RW] | |
origin | [RW] | |
raw | [RW] | |
reasoning | [RW] | |
result_info | [RW] | |
sequence | [RW] | |
title | [RW] |
Returns aBio::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
Constructs aBio::PSORT::PSORT1::Report object.
# 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
Returns aBio::PSORT::PSORT1::Report.
# File lib/bio/appl/psort/report.rb, line 31 31: def self.parser(output_report) 32: self.default_parser(output_report) 33: end