def test_isaligned(self):
seqs = fasta_io.read(StringIO())
assert seqs.isaligned()
seqs = fasta_io.read(StringIO(fasta_io.example))
assert seqs.isaligned()
seqs = fasta_io.read(StringIO(example4))
assert not seqs.isaligned()
def test_write_comments(self):
f = StringIO(example_with_optional_comments)
seqs = fasta_io.read(f)
fout = StringIO()
fasta_io.write(fout, seqs)
fout.seek(0)
seqs2 = fasta_io.read(fout)
self.assertEqual(seqs, seqs2)
self.assertEqual(seqs[1].description, seqs2[1].description)
def test_write_seq(self):
f = StringIO(fasta_io.example)
seqs = fasta_io.read(f)
fout = StringIO()
fasta_io.write(fout, seqs)
fout.seek(0)
seqs2 = fasta_io.read(fout)
self.assertEqual(seqs, seqs2)
def test_read_comments(self):
f = StringIO(example_with_optional_comments)
seqs = fasta_io.read(f)
self.assertEqual(len(seqs), 2)
self.assertEqual(seqs[1].startswith("SATVSEI"), True)
self.assertEqual(seqs[1].description.splitlines()[1],
("comment line 1 (optional)"))
def test_read(self):
f = StringIO(fasta_io.example)
seqs = fasta_io.read(f)
# print seqs
self.assertEqual(len(seqs), 3)
self.assertEqual(seqs[0].description, "Lamprey GLOBIN V - SEA LAMPREY")
self.assertEqual(seqs[0].name, "Lamprey")
self.assertEqual(len(seqs[1]), 231)
def test_read_headerless(self):
# This example has blank headers.
f = StringIO(example3)
seqs = fasta_io.read(f)
self.assertEqual(len(seqs), 4)
# print seqs
fout = StringIO()
fasta_io.write(fout, seqs)
def test_read_with_blank_line(self):
f = StringIO(example4)
seqs = fasta_io.read(f)
assert not seqs.isaligned()
self.assertEqual(len(seqs), 3)
def test_read_empty(self):
f = StringIO()
seqs = fasta_io.read(f)
assert len(seqs) == 0
def test_write_with_header(self):
f = StringIO(fasta_io.example)
seqs = fasta_io.read(f)
seqs.description = "A description\nMore description"
fout = StringIO()
fasta_io.write(fout, seqs)
def test_parse_globin(self):
# f = open_resource(__file__, "test_data", "globin.fa")
f = data_stream("globin.fa")
seqs = fasta_io.read(f, protein_alphabet)
self.assertEqual(len(seqs), 56)
f.close()