class ORFFinder
Wrapper class that processes the direct and reverse sequences
Constants
- DEFAULT_OPTIONS
Attributes
codon_table[R]
Public Class Methods
new(sequence, codon_table = 1, options = {}, logger = nil)
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# File lib/orf_finder.rb, line 17 def initialize(sequence, codon_table = 1, options = {}, logger = nil) # sequence = Bio::Sequence::NA.new(sequence) if sequence.class == String options = DEFAULT_OPTIONS.merge(options.nil? ? {} : options) # @output = {} @output[:direct] = ORF.new(sequence, options, logger) if options[:direct] # if options[:reverse] compl = sequence.complement @output[:reverse] = ORF.new(compl, options, logger) end # @codon_table = codon_table end
Public Instance Methods
aa()
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# File lib/orf_finder.rb, line 42 def aa res = {} @output.each do |key, value| res[key] = value.aa(@codon_table) res[key][:sequence] = value.sequence.translate(@codon_table).to_s end res end
direct()
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# File lib/orf_finder.rb, line 51 def direct @output[:direct] end
nt()
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# File lib/orf_finder.rb, line 33 def nt res = {} @output.each do |key, value| res[key] = value.nt(@codon_table) res[key][:sequence] = value.seq end res end
reverse()
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# File lib/orf_finder.rb, line 55 def reverse @output[:reverse] end