Class: ORFFinder

Inherits:
Object
  • Object
show all
Defined in:
lib/orf_finder.rb

Overview

Wrapper class that processes the direct and reverse sequences

Constant Summary collapse

DEFAULT_OPTIONS = 
{ start: %w(atg),
stop:  %w(tag taa tga),
reverse: true,
direct: true,
min: 6,
debug: false }

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(sequence, codon_table = 1, options = {}, logger = nil) ⇒ ORFFinder

Returns a new instance of ORFFinder.



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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

Instance Attribute Details

#codon_table ⇒ Object (readonly)

Returns the value of attribute codon_table.



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# File 'lib/orf_finder.rb', line 8

def codon_table
  @codon_table
end

Instance Method Details

#aa ⇒ Object 



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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 ⇒ Object 



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# File 'lib/orf_finder.rb', line 51

def direct
  @output[:direct]
end

#nt ⇒ Object 



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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 ⇒ Object 



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# File 'lib/orf_finder.rb', line 55

def reverse
  @output[:reverse]
end