1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
|
from io import StringIO
import pytest
from weblogo.seq import protein_alphabet
from weblogo.seq_io import clustal_io, nexus_io, plain_io
from . import data_stream
def test_read() -> None:
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_parse_StringIO() -> None:
# Bio.Nexus cannot read from a StringIO object.
f0 = data_stream("nexus/protein.nex")
f = StringIO(f0.read())
nexus_io.read(f)
f0.close()
def test_parse_fasta_fail() -> None:
with pytest.raises(ValueError):
with data_stream("globin.fa") as f:
nexus_io.read(f)
def test_parse_clustal_fail() -> None:
# should fail with parse error
with pytest.raises(ValueError):
f = StringIO(clustal_io.example)
nexus_io.read(f, protein_alphabet)
def test_parse_plain_fail() -> None:
# should fail with parse error
f = StringIO(plain_io.example)
with pytest.raises(ValueError):
nexus_io.read(f)
def test_iterseq() -> None:
f = data_stream("nexus/protein.nex")
for seq in nexus_io.iterseq(f):
pass
def test_read_alphabet() -> None:
f = data_stream("nexus/protein.nex")
seqs = nexus_io.read(f, alphabet=protein_alphabet)
# print seqs
assert len(seqs) == 10
|
