Module Bio::Sequence::SequenceMasker
In: lib/bio/sequence/sequence_masker.rb

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.

Methods

Public Instance methods

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

[Source]

    # File lib/bio/sequence/sequence_masker.rb, line 39
39:     def mask_with_enumerator(enum, mask_char)
40:       offset = 0
41:       unit = mask_char.length - 1
42:       s = self.seq.class.new(self.seq)
43:       j = 0
44:       enum.each_with_index do |item, index|
45:         if yield item then
46:           j = index + offset
47:           if j < s.length then
48:             s[j, 1] = mask_char
49:             offset += unit
50:           end
51:         end
52:       end
53:       newseq = self.dup
54:       newseq.seq = s
55:       newseq
56:     end

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

[Source]

    # File lib/bio/sequence/sequence_masker.rb, line 86
86:     def mask_with_error_probability(threshold, mask_char)
87:       values = self.error_probabilities || []
88:       mask_with_enumerator(values, mask_char) do |item|
89:         item > threshold
90:       end
91:     end

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

[Source]

    # File lib/bio/sequence/sequence_masker.rb, line 69
69:     def mask_with_quality_score(threshold, mask_char)
70:       scores = self.quality_scores || []
71:       mask_with_enumerator(scores, mask_char) do |item|
72:         item < threshold
73:       end
74:     end

[Validate]