Method: Bio::GFF::GFF3::Record::Gap#process_sequences_na

Defined in:
lib/bio/db/gff.rb

#process_sequences_na(reference, target, gap_char = '-') ⇒ Object

Processes nucleotide sequences and returns gapped sequences as an array of sequences.

Note for forward/reverse frameshift: Forward/Reverse_frameshift is simply treated as gap insertion to the target/reference sequence.

Arguments:

  • reference: reference sequence (nucleotide sequence)

  • target: target sequence (nucleotide sequence)

  • gap_char: gap character



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# File 'lib/bio/db/gff.rb', line 1717

def process_sequences_na(reference, target, gap_char = '-')
  s_ref, s_tgt = dup_seqs(reference, target)

  s_ref, s_tgt = __process_sequences(s_ref, s_tgt,
                                     gap_char, gap_char,
                                     1, 1,
                                     gap_char, gap_char)

  if $VERBOSE and s_ref.length != s_tgt.length then
    warn "returned sequences not equal length"
  end
  return s_ref, s_tgt
end