def test_parse_fasta_fail():
# should fail with parse error
with pytest.raises(ValueError):
f = StringIO(fasta_io.example)
plain_io.read(f, protein_alphabet)
with pytest.raises(ValueError):
f = StringIO(plain_io.example)
plain_io.read(f, rna_alphabet)
def test_write_seq():
f = StringIO(plain_io.example)
seqs = plain_io.read(f)
fout = StringIO()
plain_io.write(fout, seqs)
fout.seek(0)
seqs2 = plain_io.read(fout)
# print seqs[0].alphabet !=seqs2[0].alphabet
assert seqs[0].alphabet == seqs2[0].alphabet
assert seqs[0] == seqs2[0]
assert seqs == seqs2
def test_read_example():
f = StringIO(plain_io.example)
seqs = plain_io.read(f)
# print seqs
assert len(seqs) == 1
assert seqs[0].name is None
# print seqs[0]
assert len(seqs[0]) == 450
def test_write():
f = StringIO(plain_io.example)
seqs = plain_io.read(f)
fout = StringIO()
null_io.write(fout, seqs)
fout.seek(0)
assert fout.read() == ''