Class | Bio::Fasta::Report::Hit |
In: |
lib/bio/appl/fasta/format10.rb
|
Parent: | Object |
definition | [R] | |
query | [R] | |
score | [R] | |
target | [R] |
# File lib/bio/appl/fasta/format10.rb, line 111 111: def initialize(data) 112: score, query, target = data.split(/\n>/) 113: 114: @definition, *score = score.split(/\n/) 115: @score = {} 116: 117: pat = /;\s+([^:]+):\s+(.*)/ 118: 119: score.each do |x| 120: if pat.match(x) 121: @score[$1] = $2 122: end 123: end 124: 125: @query = Query.new(query) 126: @target = Target.new(target) 127: end
Bit score
# File lib/bio/appl/fasta/format10.rb, line 144 144: def bit_score 145: if @score['fa_bits'] 146: @score['fa_bits'].to_f 147: elsif @score['sw_bits'] 148: @score['sw_bits'].to_f 149: elsif @score['fx_bits'] 150: @score['fx_bits'].to_f 151: elsif @score['tx_bits'] 152: @score['tx_bits'].to_f 153: end 154: end
# File lib/bio/appl/fasta/format10.rb, line 156 156: def direction 157: @score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame'] 158: end
E-value score
# File lib/bio/appl/fasta/format10.rb, line 131 131: def evalue 132: if @score['fa_expect'] 133: @score['fa_expect'].to_f 134: elsif @score['sw_expect'] 135: @score['sw_expect'].to_f 136: elsif @score['fx_expect'] 137: @score['fx_expect'].to_f 138: elsif @score['tx_expect'] 139: @score['tx_expect'].to_f 140: end 141: end
# File lib/bio/appl/fasta/format10.rb, line 237 237: def lap_at 238: [ query_start, query_end, target_start, target_end ] 239: end
Shortcuts for the methods of Bio::Fasta::Report::Hit::Query
# File lib/bio/appl/fasta/format10.rb, line 177 177: def query_id 178: @query.entry_id 179: end
Information on matching region
# File lib/bio/appl/fasta/format10.rb, line 221 221: def query_start 222: @query.start 223: end
Smith-Waterman score
# File lib/bio/appl/fasta/format10.rb, line 161 161: def sw 162: @score['sw_score'].to_i 163: end
# File lib/bio/appl/fasta/format10.rb, line 189 189: def target_def 190: @target.definition 191: end
Shortcuts for the methods of Bio::Fasta::Report::Hit::Target
# File lib/bio/appl/fasta/format10.rb, line 199 199: def target_len 200: @target.length 201: end