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#
# = test/unit/bio/sequence/test_sequence_masker.rb - Unit test for Bio::Sequence::SequenceMasker
#
# Copyright:: Copyright (C) 2010
# Naohisa Goto <ng@bioruby.org>
# License:: The Ruby License
#
# loading helper routine for testing bioruby
require 'pathname'
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
'bioruby_test_helper.rb')).cleanpath.to_s
# libraries needed for the tests
require 'test/unit'
require 'bio/sequence'
require 'bio/sequence/sequence_masker'
module Bio
class TestSequenceMasker < Test::Unit::TestCase
def setup
s = "aaacgcattagcaccaccattaccaccacc"
@raw = s.dup.freeze
@seq = Bio::Sequence.new(s)
@seq.quality_scores =
(0...30).collect { |i| i * 3 }
@seq.error_probabilities =
(0...30).collect { |i| 10 ** -(i * 3 / 10.0) }
end
# Very simple enumerator for testing.
class SimpleEnum
include Enumerable
def initialize(ary)
@ary = ary
end
def each(&block)
@ary.each(&block)
end
end #class SimpleEnum
def test_mask_with_enumerator
enum = SimpleEnum.new((0..29).to_a)
newseq = @seq.mask_with_enumerator(enum, 'n') do |item|
i = item % 10
i == 9 || i == 0
end
expected = "naacgcattnncaccaccannaccaccacn"
assert_equal(expected, newseq.seq)
# not breaking original sequence
assert_equal(@raw, @seq.seq)
end
def test_mask_with_enumerator_longer_mask_char
enum = SimpleEnum.new((0..29).to_a)
newseq = @seq.mask_with_enumerator(enum, '-*-') do |item|
i = item % 10
i == 9 || i == 0
end
expected = "-*-aacgcatt-*--*-caccacca-*--*-accaccac-*-"
assert_equal(expected, newseq.seq)
# not breaking original sequence
assert_equal(@raw, @seq.seq)
end
def test_mask_with_enumerator_empty_mask_char
enum = SimpleEnum.new((0..29).to_a)
newseq = @seq.mask_with_enumerator(enum, '') do |item|
i = item % 10
i == 9 || i == 0
end
expected = "aacgcattcaccaccaaccaccac"
assert_equal(expected, newseq.seq)
# not breaking original sequence
assert_equal(@raw, @seq.seq)
end
def test_mask_with_enumerator_shorter
enum = SimpleEnum.new((0..10).to_a.freeze)
enum.freeze
# normal mask char
newseq = @seq.mask_with_enumerator(enum, 'n') do |item|
item > 5
end
expected = "aaacgcnnnnncaccaccattaccaccacc"
assert_equal(expected, newseq.seq)
# not breaking original sequence
assert_equal(@raw, @seq.seq)
# empty mask char
newseq = @seq.mask_with_enumerator(enum, '') do |item|
item > 5
end
expected = "aaacgccaccaccattaccaccacc"
assert_equal(expected, newseq.seq)
# not breaking original sequence
assert_equal(@raw, @seq.seq)
# longer mask char
newseq = @seq.mask_with_enumerator(enum, '-*-') do |item|
item > 5
end
expected = "aaacgc-*--*--*--*--*-caccaccattaccaccacc"
assert_equal(expected, newseq.seq)
# not breaking original sequence
assert_equal(@raw, @seq.seq)
end
def test_mask_with_enumerator_excess
enum = SimpleEnum.new((0..200).to_a.freeze)
enum.freeze
# normal mask char
newseq = @seq.mask_with_enumerator(enum, 'n') do |item|
i = item % 10
i == 9 || i == 0
end
expected = "naacgcattnncaccaccannaccaccacn"
assert_equal(expected, newseq.seq)
# not breaking original sequence
assert_equal(@raw, @seq.seq)
# empty mask char
newseq = @seq.mask_with_enumerator(enum, '') do |item|
i = item % 10
i == 9 || i == 0
end
expected = "aacgcattcaccaccaaccaccac"
assert_equal(expected, newseq.seq)
# not breaking original sequence
assert_equal(@raw, @seq.seq)
# longer mask char
newseq = @seq.mask_with_enumerator(enum, '-*-') do |item|
i = item % 10
i == 9 || i == 0
end
expected = "-*-aacgcatt-*--*-caccacca-*--*-accaccac-*-"
assert_equal(expected, newseq.seq)
# not breaking original sequence
assert_equal(@raw, @seq.seq)
end
def test_mask_with_quality_score
newseq = @seq.mask_with_quality_score(30, 'n')
expected = "nnnnnnnnnngcaccaccattaccaccacc"
assert_equal(expected, newseq.seq)
# not breaking original sequence
assert_equal(@raw, @seq.seq)
end
def test_mask
newseq = @seq.mask_with_quality_score(30, 'n')
expected = "nnnnnnnnnngcaccaccattaccaccacc"
assert_equal(expected, newseq.seq)
# not breaking original sequence
assert_equal(@raw, @seq.seq)
end
def test_mask_with_error_probability
newseq = @seq.mask_with_error_probability(0.001, 'n')
expected = "nnnnnnnnnngcaccaccattaccaccacc"
assert_equal(expected, newseq.seq)
# not breaking original sequence
assert_equal(@raw, @seq.seq)
end
end #class TestSequenceMasker
end #module Bio
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