def test_write_alignment(self):
# Default causes no interleave (columns <= 1000)
records = [
SeqRecord(Seq("ATGCTGCTGA" * 90),
id=_id,
annotations={"molecule_type": "DNA"})
for _id in ["foo", "bar", "baz"]
]
a = MultipleSeqAlignment(records)
handle = StringIO()
NexusWriter(handle).write_alignment(a)
handle.seek(0)
data = handle.read()
self.assertIn("ATGCTGCTGA" * 90, data)
# Default causes interleave (columns > 1000)
records = [
SeqRecord(Seq("ATGCTGCTGA" * 110),
id=_id,
annotations={"molecule_type": "DNA"})
for _id in ["foo", "bar", "baz"]
]
a = MultipleSeqAlignment(records)
handle = StringIO()
NexusWriter(handle).write_alignment(a)
handle.seek(0)
data = handle.read()
self.assertNotIn("ATGCTGCTGA" * 90, data)
self.assertIn("ATGCTGCTGA" * 7, data)
# Override interleave: True
records = [
SeqRecord(Seq("ATGCTGCTGA" * 9),
id=_id,
annotations={"molecule_type": "DNA"})
for _id in ["foo", "bar", "baz"]
]
a = MultipleSeqAlignment(records)
handle = StringIO()
NexusWriter(handle).write_alignment(a, interleave=True)
handle.seek(0)
data = handle.read()
self.assertNotIn("ATGCTGCTGA" * 9, data)
self.assertIn("ATGCTGCTGA" * 7, data)
# Override interleave: False
records = [
SeqRecord(Seq("ATGCTGCTGA" * 110),
id=_id,
annotations={"molecule_type": "DNA"})
for _id in ["foo", "bar", "baz"]
]
a = MultipleSeqAlignment(records)
handle = StringIO()
NexusWriter(handle).write_alignment(a, interleave=False)
handle.seek(0)
data = handle.read()
self.assertIn("ATGCTGCTGA" * 110, data)
def test_write_alignment(self):
# Default causes no interleave (columns <= 1000)
records = [
SeqRecord(Seq("ATGCTGCTGA" * 90, alphabet=ambiguous_dna), id=_id)
for _id in ["foo", "bar", "baz"]
]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_alignment(a)
handle.seek(0)
data = handle.read()
self.assertIn("ATGCTGCTGA" * 90, data)
# Default causes interleave (columns > 1000)
records = [
SeqRecord(Seq("ATGCTGCTGA" * 110, alphabet=ambiguous_dna), id=_id)
for _id in ["foo", "bar", "baz"]
]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_alignment(a)
handle.seek(0)
data = handle.read()
self.assertNotIn("ATGCTGCTGA" * 90, data)
self.assertIn("ATGCTGCTGA" * 7, data)
# Override interleave: True
records = [
SeqRecord(Seq("ATGCTGCTGA" * 9, alphabet=ambiguous_dna), id=_id)
for _id in ["foo", "bar", "baz"]
]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_alignment(a, interleave=True)
handle.seek(0)
data = handle.read()
self.assertNotIn("ATGCTGCTGA" * 9, data)
self.assertIn("ATGCTGCTGA" * 7, data)
# Override interleave: False
records = [
SeqRecord(Seq("ATGCTGCTGA" * 110, alphabet=ambiguous_dna), id=_id)
for _id in ["foo", "bar", "baz"]
]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_alignment(a, interleave=False)
handle.seek(0)
data = handle.read()
self.assertIn("ATGCTGCTGA" * 110, data)
def test_multiple_output(self):
records = [
SeqRecord(Seq("ATGCTGCTGAT", alphabet=ambiguous_dna), id="foo"),
SeqRecord(Seq("ATGCTGCAGAT", alphabet=ambiguous_dna), id="bar"),
SeqRecord(Seq("ATGCTGCGGAT", alphabet=ambiguous_dna), id="baz")
]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_file([a])
handle.seek(0)
data = handle.read()
self.assertTrue(data.startswith("#NEXUS\nbegin data;\n"), data)
self.assertTrue(data.endswith("end;\n"), data)
handle = StringIO()
with self.assertRaises(ValueError):
NexusWriter(handle).write_file([a, a])
def test_multiple_output(self):
records = [SeqRecord(Seq("ATGCTGCTGAT", alphabet=ambiguous_dna), id="foo"),
SeqRecord(Seq("ATGCTGCAGAT", alphabet=ambiguous_dna), id="bar"),
SeqRecord(Seq("ATGCTGCGGAT", alphabet=ambiguous_dna), id="baz")]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_file([a])
handle.seek(0)
data = handle.read()
self.assertTrue(data.startswith("#NEXUS\nbegin data;\n"), data)
self.assertTrue(data.endswith("end;\n"), data)
handle = StringIO()
try:
NexusWriter(handle).write_file([a, a])
assert False, "Should have rejected more than one alignment!"
except ValueError:
pass
def test_multiple_output(self):
records = [
SeqRecord(Seq("ATGCTGCTGAT"),
id="foo",
annotations={"molecule_type": "DNA"}),
SeqRecord(Seq("ATGCTGCAGAT"),
id="bar",
annotations={"molecule_type": "DNA"}),
SeqRecord(Seq("ATGCTGCGGAT"),
id="baz",
annotations={"molecule_type": "DNA"}),
]
a = MultipleSeqAlignment(records)
handle = StringIO()
NexusWriter(handle).write_file([a])
handle.seek(0)
data = handle.read()
self.assertTrue(data.startswith("#NEXUS\nbegin data;\n"), data)
self.assertTrue(data.endswith("end;\n"), data)
handle = StringIO()
with self.assertRaises(ValueError):
NexusWriter(handle).write_file([a, a])
