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_iupac_characters(self):
exp = {
'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N',
'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'X', 'Y', 'Z', 'a', 'b',
'c', 'd', 'e', 'f', 'g', 'h', 'i', 'k', 'l', 'm', 'n', 'p', 'q',
'r', 's', 't', 'v', 'w', 'x', 'y', 'z'
}
self.assertEqual(self.p1.iupac_characters(), exp)
self.assertEqual(ProteinSequence.iupac_characters(), exp)
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_iupac_characters(self):
exp = {
'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N',
'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'X', 'Y', 'Z', 'a', 'b', 'c',
'd', 'e', 'f', 'g', 'h', 'i', 'k', 'l', 'm', 'n', 'p', 'q', 'r',
's', 't', 'v', 'w', 'x', 'y', 'z'
}
self.assertEqual(self.p1.iupac_characters(), exp)
self.assertEqual(ProteinSequence.iupac_characters(), exp)
def test_iupac_degeneracies(self):
exp = {
'B': set(['D', 'N']), 'Z': set(['E', 'Q']),
'X': set(['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M',
'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']),
'b': set(['d', 'n']), 'z': set(['e', 'q']),
'x': set(['a', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'k', 'l', 'm',
'n', 'p', 'q', 'r', 's', 't', 'v', 'w', 'y']),
}
self.assertEqual(self.p1.iupac_degeneracies(), exp)
self.assertEqual(ProteinSequence.iupac_degeneracies(), exp)
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_iupac_degeneracies(self):
exp = {
'B':
set(['D', 'N']),
'Z':
set(['E', 'Q']),
'X':
set([
'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N',
'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'
]),
'b':
set(['d', 'n']),
'z':
set(['e', 'q']),
'x':
set([
'a', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'k', 'l', 'm', 'n',
'p', 'q', 'r', 's', 't', 'v', 'w', 'y'
]),
}
self.assertEqual(self.p1.iupac_degeneracies(), exp)
self.assertEqual(ProteinSequence.iupac_degeneracies(), exp)
def test_iupac_degenerate_characters(self):
exp = set(['B', 'X', 'Z', 'b', 'x', 'z'])
self.assertEqual(self.p1.iupac_degenerate_characters(), exp)
self.assertEqual(ProteinSequence.iupac_degenerate_characters(), exp)
def test_iupac_standard_characters(self):
exp = set("ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy")
self.assertEqual(self.p1.iupac_standard_characters(), exp)
self.assertEqual(ProteinSequence.iupac_standard_characters(), exp)
class ProteinSequenceTests(TestCase):
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_alphabet(self):
exp = {
'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N',
'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'X', 'Y', 'Z', 'a', 'b', 'c',
'd', 'e', 'f', 'g', 'h', 'i', 'k', 'l', 'm', 'n', 'p', 'q', 'r',
's', 't', 'v', 'w', 'x', 'y', 'z'
}
self.assertEqual(self.p1.alphabet(), exp)
self.assertEqual(ProteinSequence.alphabet(), exp)
def test_gap_alphabet(self):
self.assertEqual(self.p1.gap_alphabet(), set('-.'))
def test_iupac_standard_characters(self):
exp = set("ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy")
self.assertEqual(self.p1.iupac_standard_characters(), exp)
self.assertEqual(ProteinSequence.iupac_standard_characters(), exp)
def test_iupac_degeneracies(self):
exp = {
'B': set(['D', 'N']), 'Z': set(['E', 'Q']),
'X': set(['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M',
'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']),
'b': set(['d', 'n']), 'z': set(['e', 'q']),
'x': set(['a', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'k', 'l', 'm',
'n', 'p', 'q', 'r', 's', 't', 'v', 'w', 'y']),
}
self.assertEqual(self.p1.iupac_degeneracies(), exp)
self.assertEqual(ProteinSequence.iupac_degeneracies(), exp)
def test_iupac_degenerate_characters(self):
exp = set(['B', 'X', 'Z', 'b', 'x', 'z'])
self.assertEqual(self.p1.iupac_degenerate_characters(), exp)
self.assertEqual(ProteinSequence.iupac_degenerate_characters(), exp)
def test_iupac_characters(self):
exp = {
'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N',
'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'X', 'Y', 'Z', 'a', 'b',
'c', 'd', 'e', 'f', 'g', 'h', 'i', 'k', 'l', 'm', 'n', 'p', 'q',
'r', 's', 't', 'v', 'w', 'x', 'y', 'z'
}
self.assertEqual(self.p1.iupac_characters(), exp)
self.assertEqual(ProteinSequence.iupac_characters(), exp)
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)
def test_iupac_standard_characters(self):
exp = set("ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy")
self.assertEqual(self.p1.iupac_standard_characters(), exp)
self.assertEqual(ProteinSequence.iupac_standard_characters(), exp)
class ProteinSequenceTests(TestCase):
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_alphabet(self):
exp = {
'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N',
'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'X', 'Y', 'Z', 'a', 'b', 'c',
'd', 'e', 'f', 'g', 'h', 'i', 'k', 'l', 'm', 'n', 'p', 'q', 'r',
's', 't', 'v', 'w', 'x', 'y', 'z'
}
self.assertEqual(self.p1.alphabet(), exp)
self.assertEqual(ProteinSequence.alphabet(), exp)
def test_gap_alphabet(self):
self.assertEqual(self.p1.gap_alphabet(), set('-.'))
def test_iupac_standard_characters(self):
exp = set("ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy")
self.assertEqual(self.p1.iupac_standard_characters(), exp)
self.assertEqual(ProteinSequence.iupac_standard_characters(), exp)
def test_iupac_degeneracies(self):
exp = {
'B':
set(['D', 'N']),
'Z':
set(['E', 'Q']),
'X':
set([
'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N',
'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'
]),
'b':
set(['d', 'n']),
'z':
set(['e', 'q']),
'x':
set([
'a', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'k', 'l', 'm', 'n',
'p', 'q', 'r', 's', 't', 'v', 'w', 'y'
]),
}
self.assertEqual(self.p1.iupac_degeneracies(), exp)
self.assertEqual(ProteinSequence.iupac_degeneracies(), exp)
def test_iupac_degenerate_characters(self):
exp = set(['B', 'X', 'Z', 'b', 'x', 'z'])
self.assertEqual(self.p1.iupac_degenerate_characters(), exp)
self.assertEqual(ProteinSequence.iupac_degenerate_characters(), exp)
def test_iupac_characters(self):
exp = {
'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N',
'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'X', 'Y', 'Z', 'a', 'b', 'c',
'd', 'e', 'f', 'g', 'h', 'i', 'k', 'l', 'm', 'n', 'p', 'q', 'r',
's', 't', 'v', 'w', 'x', 'y', 'z'
}
self.assertEqual(self.p1.iupac_characters(), exp)
self.assertEqual(ProteinSequence.iupac_characters(), exp)
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)
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)
def test_iupac_degenerate_characters(self):
exp = set(['B', 'X', 'Z', 'b', 'x', 'z'])
self.assertEqual(self.p1.iupac_degenerate_characters(), exp)
self.assertEqual(ProteinSequence.iupac_degenerate_characters(), exp)