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.
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
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
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
Generated with the Darkfish Rdoc Generator 2.