module Bio::Sequence::SequenceMasker

Bio::Sequence::SequenceMasker is a mix-in module to provide helpful methods for masking a sequence.

It is only expected to be included in Bio::Sequence. In the future, methods in this module might be moved to Bio::Sequence or other module and this module might be removed. Please do not depend on this module.

Public Instance Methods

mask_with_enumerator(enum, mask_char) { |item then j = index + offset| ... } click to toggle source

Masks the sequence with each value in the enum. The enum<em> should be an array or enumerator. A block must be given. When the block returns true, the sequence is masked with <em>mask_char.


Arguments:

  • (required) enum : Enumerator

  • (required) mask_char : (String) character used for masking

Returns

Bio::Sequence object

# File lib/bio/sequence/sequence_masker.rb, line 42
def mask_with_enumerator(enum, mask_char)
  offset = 0
  unit = mask_char.length - 1
  s = self.seq.class.new(self.seq)
  j = 0
  enum.each_with_index do |item, index|
    if yield item then
      j = index + offset
      if j < s.length then
        s[j, 1] = mask_char
        offset += unit
      end
    end
  end
  newseq = self.dup
  newseq.seq = s
  newseq
end
mask_with_error_probability(threshold, mask_char) click to toggle source

Masks high error-probability sequence regions. For each sequence position, if the error probability is larger than the threshold, the sequence in the position is replaced with mask_char.


Arguments:

  • (required) threshold : (Numeric) threshold

  • (required) mask_char : (String) character used for masking

Returns

Bio::Sequence object

# File lib/bio/sequence/sequence_masker.rb, line 89
def mask_with_error_probability(threshold, mask_char)
  values = self.error_probabilities || []
  mask_with_enumerator(values, mask_char) do |item|
    item > threshold
  end
end
mask_with_quality_score(threshold, mask_char) click to toggle source

Masks low quality sequence regions. For each sequence position, if the quality score is smaller than the threshold, the sequence in the position is replaced with mask_char.

Note: This method does not care quality_score_type.


Arguments:

  • (required) threshold : (Numeric) threshold

  • (required) mask_char : (String) character used for masking

Returns

Bio::Sequence object

# File lib/bio/sequence/sequence_masker.rb, line 72
def mask_with_quality_score(threshold, mask_char)
  scores = self.quality_scores || []
  mask_with_enumerator(scores, mask_char) do |item|
    item < threshold
  end
end