Module: Bio::Big::TranslationAdapter

Included in:
Nucleotide::Translate
Defined in:
lib/bigbio/adapters/translate.rb

Constant Summary collapse

VALID_FRAME_VALUES = 
[ 0, -1, -2, -3, 1, 2, 3 ]

Class Method Summary collapse

Class Method Details

.pre_translate(seq, label) ⇒ Object

Precompile sequence for EMBOSS



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# File 'lib/bigbio/adapters/translate.rb', line 17

def self.pre_translate seq,label
  if Environment.instance.biolib
    Biolib::Emboss.ajSeqNewNameC(seq,"Test sequence")
  else
    nil
  end
end

.translate(trn_table, frame, seq, pre_seq = nil) ⇒ Object

Translate using frame (pre_seq is only used for EMBOSS)

Valid frame values are 0,1,2,3 and -1,-2,-3, where 0 and 1 are the standard reading frame. The negative values translate the reverse complement of the strand.



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# File 'lib/bigbio/adapters/translate.rb', line 30

def self.translate trn_table, frame, seq, pre_seq = nil
  raise "Illegal frame #{frame}" if VALID_FRAME_VALUES.index(frame) == nil
  frame = 1 if frame == 0
  if Environment.instance.biolib
    # Using EMBOSS for translation
    ajpseq = pre_seq
    if not pre_seq
      ajpseq = Biolib::Emboss.ajSeqNewNameC(seq,"Test sequence")
    end
    ajpseqt  = Biolib::Emboss.ajTrnSeqOrig(trn_table,ajpseq,frame)
    Biolib::Emboss.ajSeqGetSeqCopyC(ajpseqt)
  else
    # Using BioRuby for translation
    ntseq = if frame > 0 
      Bio::Sequence::NA.new(seq[frame-1..-1])
    else
      # This to match EMBOSS frames
      rframe =
        case frame
          when -2 
            -3 
          when -3
            -2
          else 
            -1
        end
      Bio::Sequence::NA.new(seq[0..rframe]).reverse_complement
    end
    # pp ntseq
    ntseq.translate.to_s
  end
end

.translation_table(num) ⇒ Object 



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# File 'lib/bigbio/adapters/translate.rb', line 10

def self.translation_table num
  if Environment.instance.biolib
    Biolib::Emboss.ajTrnNewI(num)
  end
end