Class: Bio::Sequence::NA

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/sequence/emboss_six_frame_nucleotide_sequences.rb

Instance Method Summary collapse

Instance Method Details

#nucleotide_sequence_of_transeq_translation(frame) ⇒ Object

Translate this nucleotide sequence into a particular frame, but return the nucleotide sequence of that translation, rather the amino acid sequence. The frame returned aligns with the frames that are generated by the EMBOSS package program transeq. Note that these are different than the translations generated by bioruby itself.

Bio::Sequence::NA.new('ATGATG').nucleotide_sequence_of_transeq_translation(1) => Bio::Sequence::NA.new('ATGATG')
Bio::Sequence::NA.new('ATGATG').nucleotide_sequence_of_transeq_translation(2) => Bio::Sequence::NA.new('TGATG')
Bio::Sequence::NA.new('ATGATG').nucleotide_sequence_of_transeq_translation(4) => Bio::Sequence::NA.new('CATCAT')



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# File 'lib/bio/sequence/emboss_six_frame_nucleotide_sequences.rb', line 15

def nucleotide_sequence_of_transeq_translation(frame)
  unless [-1,-2,-3,1,2,3,4,5,6].include?(frame) #error checking
    raise Exception, "unexpected frame for translation: `#{frame.inspect}'"
  end

  # Offset table for reverse frames. indexed by frame-4, then length%3
  offset_table = [[0,-2,-1],[-1,0,-2],[-2,-1,0]]

  # deal with the easy case of translating in the forward direction.
  if frame < 4
    return Bio::Sequence::NA.new(self[frame-1..length-1])
  end

  # translate negatives into positives for reverse sequences
  frame = 6 if frame == -3
  frame = 5 if frame == -2
  frame = 4 if frame == -1

  remainder = length%3
  offset = offset_table[remainder][frame-4]
  return Bio::Sequence::NA.new(self[0..length-1+offset].reverse_complement)
end