def test_read():
f = data_stream("nexus/protein.nex")
seqs = nexus_io.read(f)
# print seqs
assert len(seqs) == 10
assert seqs[0].name == "Cow"
assert len(seqs[1]) == 234
assert str(seqs[0][0:10]) == "MAYPMQLGFQ"
f.close()
def test_read_alphabet():
f = data_stream("nexus/protein.nex")
seqs = nexus_io.read(f, alphabet=protein_alphabet)
# print seqs
assert len(seqs) == 10
def test_parse_plain_fail():
# should fail with parse error
f = StringIO(plain_io.example)
with pytest.raises(ValueError):
nexus_io.read(f)
def test_parse_clustal_fail():
# should fail with parse error
with pytest.raises(ValueError):
f = StringIO(clustal_io.example)
nexus_io.read(f, protein_alphabet)
def test_parse_fasta_fail():
with pytest.raises(ValueError):
with data_stream("globin.fa") as f:
nexus_io.read(f)
def test_parse_StringIO():
# Bio.Nexus cannot read from a StringIO object.
f0 = data_stream("nexus/protein.nex")
f = StringIO(f0.read())
nexus_io.read(f)
f0.close()