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#
# = bio/sequence/sequence_masker.rb - Sequence masking helper methods
#
# Copyright:: Copyright (C) 2010
# Naohisa Goto <ng@bioruby.org>
# License:: The Ruby License
#
# == Description
#
# Bio::Sequence::SequenceMasker is a mix-in module to provide helpful
# methods for masking a sequence.
#
# For details, see documentation of Bio::Sequence::SequenceMasker.
#
module Bio
require 'bio/sequence' unless const_defined?(:Sequence)
class Sequence
# 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.
#
module SequenceMasker
# Masks the sequence with each value in the <em>enum</em>.
# The <em>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</em>.
# ---
# *Arguments*:
# * (required) <em>enum</em> : Enumerator
# * (required) <em>mask_char</em> : (String) character used for masking
# *Returns*:: Bio::Sequence object
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 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
# <em>mask_char</em>.
#
# Note: This method does not care quality_score_type.
# ---
# *Arguments*:
# * (required) <em>threshold</em> : (Numeric) threshold
# * (required) <em>mask_char</em> : (String) character used for masking
# *Returns*:: Bio::Sequence object
def mask_with_quality_score(threshold, mask_char)
scores = self.quality_scores || []
mask_with_enumerator(scores, mask_char) do |item|
item < threshold
end
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
# <em>mask_char</em>.
#
# ---
# *Arguments*:
# * (required) <em>threshold</em> : (Numeric) threshold
# * (required) <em>mask_char</em> : (String) character used for masking
# *Returns*:: Bio::Sequence object
def mask_with_error_probability(threshold, mask_char)
values = self.error_probabilities || []
mask_with_enumerator(values, mask_char) do |item|
item > threshold
end
end
end #module SequenceMasker
end #class Sequence
end #module Bio
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