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
42 def mask_with_enumerator(enum, mask_char)
43   offset = 0
44   unit = mask_char.length - 1
45   s = self.seq.class.new(self.seq)
46   j = 0
47   enum.each_with_index do |item, index|
48     if yield item then
49       j = index + offset
50       if j < s.length then
51         s[j, 1] = mask_char
52         offset += unit
53       end
54     end
55   end
56   newseq = self.dup
57   newseq.seq = s
58   newseq
59 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
89 def mask_with_error_probability(threshold, mask_char)
90   values = self.error_probabilities || []
91   mask_with_enumerator(values, mask_char) do |item|
92     item > threshold
93   end
94 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
72 def mask_with_quality_score(threshold, mask_char)
73   scores = self.quality_scores || []
74   mask_with_enumerator(scores, mask_char) do |item|
75     item < threshold
76   end
77 end