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require 'test/unit'
require 'jellyfish'
class TestStringMers < Test::Unit::TestCase
def setup
bases = "ACGTacgt"
@str = (0..1000).map { bases[rand(bases.size())] }.join("")
Jellyfish::MerDNA::k(rand(100) + 10)
end
def test_all_mers
count = 0
m2 = Jellyfish::MerDNA.new
@str.mers.each_with_index { |m, i|
assert_equal m.to_s, @str[i, Jellyfish::MerDNA::k()].upcase
m2.set @str[i, Jellyfish::MerDNA::k()]
assert_equal m2, m
count += 1
}
assert_equal @str.size - Jellyfish::MerDNA::k() + 1, count
end
def test_canonical_mers
count = 0
m2 = Jellyfish::MerDNA.new
@str.canonicals { |m|
m2.set @str[count, Jellyfish::MerDNA::k()]
cm2 = m2.get_reverse_complement
assert(m2 == m || m == cm2)
assert(!(m > m2) && !(m > cm2));
count += 1
}
assert_equal @str.size - Jellyfish::MerDNA::k() + 1, count
end
end
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