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import pytest
from pbcore import sequence
class TestReverseComplement:
SEQUENCE = "GATTACA" * 20
REVERSE = "ACATTAG" * 20
COMPLEMENT = "CTAATGT" * 20
REVERSE_COMPLEMENT = "TGTAATC" * 20
IUPAC_SEQUENCE = "ACTURY" * 20
IUPAC_COMPLEMENT = "TGANNN" * 20
IUPAC_REVERSE_COMPLEMENT = "NNNAGT" * 20
BAD_SEQUENCE = "AGCTQ" * 20 # contains non-IUPAC char
def test_reverse(self):
assert self.SEQUENCE == sequence.reverse(
sequence.reverse(self.SEQUENCE))
assert self.REVERSE == sequence.reverse(self.SEQUENCE)
assert self.COMPLEMENT == sequence.reverse(self.REVERSE_COMPLEMENT)
def test_complement(self):
assert self.SEQUENCE == sequence.complement(self.COMPLEMENT)
assert self.COMPLEMENT == sequence.complement(self.SEQUENCE)
assert self.REVERSE == sequence.complement(self.REVERSE_COMPLEMENT)
def test_reverseComplement(self):
assert self.REVERSE_COMPLEMENT == sequence.reverseComplement(
self.SEQUENCE)
assert self.SEQUENCE == sequence.reverseComplement(
self.REVERSE_COMPLEMENT)
def test_iupac(self):
assert self.IUPAC_COMPLEMENT == sequence.complement(
self.IUPAC_SEQUENCE)
assert self.IUPAC_REVERSE_COMPLEMENT == sequence.reverseComplement(
self.IUPAC_SEQUENCE)
def test_complement_error(self):
with pytest.raises(ValueError):
sequence.complement(self.BAD_SEQUENCE)
def test_reverse_complement_error(self):
with pytest.raises(ValueError):
sequence.reverseComplement(self.BAD_SEQUENCE)
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