Class: GeneValidator::Validations
- Inherits:
-
Object
- Object
- GeneValidator::Validations
- Extended by:
- Forwardable
- Defined in:
- lib/genevalidator/validation.rb
Overview
Class that initalises a separate Validate.new() instance for each query.
Instance Method Summary collapse
-
#check_if_maker_input? ⇒ Boolean
Adds ‘maker’ to @opt if the first definiton in the input fasta file contains MAKER’s QI (quality index) score.
-
#get_info_on_query_sequence(seq_type = , index = ) ⇒ Object
get info about the query.
-
#initialize ⇒ Validations
constructor
A new instance of Validations.
- #parse_next_iteration(iterator, prediction) ⇒ Object
- #run_validations(iterator) ⇒ Object
Constructor Details
#initialize ⇒ Validations
Returns a new instance of Validations.
28 29 30 31 32 |
# File 'lib/genevalidator/validation.rb', line 28 def initialize @opt = opt @config = config @query_idx = query_idx end |
Instance Method Details
#check_if_maker_input? ⇒ Boolean
Adds ‘maker’ to @opt if the first definiton in the input fasta file contains MAKER’s QI (quality index) score
86 87 88 89 90 91 92 93 94 95 96 |
# File 'lib/genevalidator/validation.rb', line 86 def check_if_maker_input? query = GeneValidator.extract_input_fasta_sequence(0) parse_query = query.scan(/>([^\n]*)\n([A-Za-z\n]*)/)[0] definition = parse_query[0].delete("\n") number = '-?\d*\.?\d*' qi_match = definition.match(/QI:#{number}\|#{number}\|#{number}\| #{number}\|#{number}\|#{number}\| #{number}\|#{number}\|#{number}/x) return if qi_match.nil? @opt[:validations] << 'maker_qi' end |
#get_info_on_query_sequence(seq_type = , index = ) ⇒ Object
get info about the query
69 70 71 72 73 74 75 76 77 78 79 80 81 82 |
# File 'lib/genevalidator/validation.rb', line 69 def get_info_on_query_sequence(seq_type = @config[:type], index = @config[:idx]) query = GeneValidator.extract_input_fasta_sequence(index) parse_query = query.scan(/>([^\n]*)\n([A-Za-z\n]*)/)[0] prediction = Query.new prediction.definition = parse_query[0].delete("\n") prediction.identifier = prediction.definition.gsub(/ .*/, '') prediction.type = seq_type prediction.raw_sequence = parse_query[1].delete("\n") prediction.length_protein = prediction.raw_sequence.length prediction.length_protein /= 3 if seq_type == :nucleotide prediction end |
#parse_next_iteration(iterator, prediction) ⇒ Object
98 99 100 101 102 103 104 105 |
# File 'lib/genevalidator/validation.rb', line 98 def parse_next_iteration(iterator, prediction) iterator.next if @config[:idx] < @config[:start_idx] if @opt[:blast_xml_file] BlastUtils.parse_next(iterator) elsif @opt[:blast_tabular_file] iterator.parse_next(prediction.identifier) end end |
#run_validations(iterator) ⇒ Object
36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 |
# File 'lib/genevalidator/validation.rb', line 36 def run_validations(iterator) p = Pool.new(@opt[:num_threads]) if @opt[:num_threads] > 1 check_if_maker_input? while @config[:idx] + 1 < @query_idx.length prediction = get_info_on_query_sequence @config[:idx] += 1 blast_hits = parse_next_iteration(iterator, prediction) if blast_hits.nil? @config[:idx] -= 1 break end arr_idx = @config[:idx] - 1 next unless @config[:json_output][arr_idx].nil? if @opt[:num_threads] == 1 Validate.new.validate(prediction, blast_hits, @config[:idx]) else p.schedule(prediction, blast_hits, @config[:idx]) do |pred, hits, idx| Validate.new.validate(pred, hits, idx) end end end ensure p.shutdown if @opt[:num_threads] > 1 end |