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import nose
from nose.tools import assert_equal, assert_true, assert_false
from pbcore import sequence
class TestReverseComplement:
def setup(self):
self.sequence = "GATTACA" * 20
self.reverse = "ACATTAG" * 20
self.complement = "CTAATGT" * 20
self.reverse_complement = "TGTAATC" * 20
self.iupac_sequence = "ACTURY" * 20
self.iupac_complement = "TGANNN" * 20
self.iupac_reverse_complement = "NNNAGT" * 20
self.bad_sequence = "AGCTQ" * 20 # contains non-IUPAC char
def test_reverse(self):
assert_equal(self.sequence,
sequence.reverse(sequence.reverse(self.sequence)))
assert_equal(self.reverse,
sequence.reverse(self.sequence))
assert_equal(self.complement,
sequence.reverse(self.reverse_complement))
def test_complement(self):
assert_equal(self.sequence,
sequence.complement(self.complement))
assert_equal(self.complement,
sequence.complement(self.sequence))
assert_equal(self.reverse,
sequence.complement(self.reverse_complement))
def test_reverseComplement(self):
assert_equal(self.reverse_complement,
sequence.reverseComplement(self.sequence))
assert_equal(self.sequence,
sequence.reverseComplement(self.reverse_complement))
def test_iupac(self):
assert_equal(self.iupac_complement,
sequence.complement(self.iupac_sequence))
assert_equal(self.iupac_reverse_complement,
sequence.reverseComplement(self.iupac_sequence))
@nose.tools.raises(ValueError)
def test_complement_error(self):
sequence.complement(self.bad_sequence)
@nose.tools.raises(ValueError)
def test_reverse_complement_error(self):
sequence.reverseComplement(self.bad_sequence)
class TestSplitRecordName:
def setup(self):
pass
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