def setUp(self):
self.empty = ProteinSequence('')
self.p1 = ProteinSequence('GREG')
self.p2 = ProteinSequence('PRTEINSEQNCE',
id="test-seq-2",
description="A test sequence")
self.p3 = ProteinSequence('PROTEIN',
id="bad-seq-1",
description="Not a protein sequence")
def test_alignment_to_fastq_kwargs_passed(self):
for components, kwargs_expected_fp in self.valid_files:
for kwargs, expected_fp in kwargs_expected_fp:
obj = Alignment([
ProteinSequence(c[2],
id=c[0],
description=c[1],
quality=c[3]) for c in components
])
fh = StringIO()
_alignment_to_fastq(obj, fh, **kwargs)
observed = fh.getvalue()
fh.close()
with open(expected_fp, 'U') as f:
expected = f.read()
self.assertEqual(observed, expected)
def test_nondegenerates(self):
exp = [ProteinSequence('AD'), ProteinSequence('AN')]
# Sort based on sequence string, as order is not guaranteed.
obs = sorted(ProteinSequence('AB').nondegenerates(), key=str)
self.assertEqual(obs, exp)
