Module: BioDSL::Digest

Included in:
Seq
Defined in:
lib/BioDSL/seq/digest.rb

Overview

Namespace for Digest.

Instance Method Summary collapse

Instance Method Details

#each_digest(pattern, cut_pos) {|subseq| ... } ⇒ Object

Method to get the next digestion product from a sequence.

Yields:

  • (subseq) 


36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
 
# File 'lib/BioDSL/seq/digest.rb', line 36

def each_digest(pattern, cut_pos)
  return to_enum(:each_digest, pattern, cut_pos) unless block_given?
  pattern = disambiguate(pattern)
  offset  = 0

  seq.upcase.scan pattern do
    pos = $`.length + cut_pos

    if pos >= 0 && pos < length - 2
      subseq = self[offset...pos]
      subseq.seq_name = "#{seq_name}[#{offset}-#{pos - offset - 1}]"

      yield subseq
    end

    offset = pos
  end

  offset = 0 if offset < 0 || offset > length
  subseq = self[offset..-1]
  subseq.seq_name = "#{seq_name}[#{offset}-#{length - 1}]"

  yield subseq
end