def test_concat_validates_type(self):
"""raises TypeError if not known alignment type"""
data = [
{
"seq1": "AAA",
"seq2": "AAA",
"seq3": "AAA"
},
make_aligned_seqs(
data={
"seq1": "TTT",
"seq2": "TTT",
"seq3": "TTT",
"seq4": "TTT"
},
moltype=DNA,
),
]
ccat = sample.concat()
# triggered by first record
with self.assertRaises(TypeError):
ccat(data)
# triggered by second record
with self.assertRaises(TypeError):
ccat(data[::-1])
# triggered by no data
with self.assertRaises(ValueError):
ccat([])
def test_concat_handles_moltype(self):
"""coerces to type"""
alns = [
make_aligned_seqs(data=d, moltype=DNA) for d in [
{
"seq1": "AAA",
"seq2": "AAA",
"seq3": "AAA"
},
{
"seq1": "TTT",
"seq2": "TTT",
"seq3": "TTT",
"seq4": "TTT"
},
{
"seq1": "CC",
"seq2": "CC",
"seq3": "CC"
},
]
]
ccat = sample.concat()
got = ccat(alns)
self.assertIsInstance(got.moltype, type(DNA))
def test_concat(self):
"""returns concatenated alignment"""
alns = [
make_aligned_seqs(data=d, moltype=DNA) for d in [
{
"seq1": "AAA",
"seq2": "AAA",
"seq3": "AAA"
},
{
"seq1": "TTT",
"seq2": "TTT",
"seq3": "TTT",
"seq4": "TTT"
},
{
"seq1": "CC",
"seq2": "CC",
"seq3": "CC"
},
]
]
ccat = sample.concat(intersect=True)
got = ccat(alns)
self.assertEqual(got.to_dict(), {
"seq1": "AAATTTCC",
"seq2": "AAATTTCC",
"seq3": "AAATTTCC"
})
ccat = sample.concat(intersect=False)
got = ccat(alns)
self.assertEqual(
got.to_dict(),
{
"seq1": "AAATTTCC",
"seq2": "AAATTTCC",
"seq3": "AAATTTCC",
"seq4": "???TTT??",
},
)