def test_read_3(self):
msa = """CLUSTAL FORMAT for
seq_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
seq_1 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
seq_2 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
seq_0 AAAAAAAAA
seq_1 BBBBBBBBB
seq_2 CCCCCCCCC
"""
f_name = create_tmp_f(content=msa)
parser = ClustalParser()
with open(f_name, 'r') as f_in:
sequence_file = parser.read(f_in)
for i, sequence_entry in enumerate(sequence_file):
if i == 0:
self.assertEqual('seq_0', sequence_entry.id)
self.assertEqual(
'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA',
sequence_entry.seq)
elif i == 1:
self.assertEqual('seq_1', sequence_entry.id)
self.assertEqual(
'BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB',
sequence_entry.seq)
elif i == 2:
self.assertEqual('seq_2', sequence_entry.id)
self.assertEqual(
'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC',
sequence_entry.seq)
os.unlink(f_name)
def test_read_3(self):
msa = """CLUSTAL FORMAT for
seq_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
seq_1 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
seq_2 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
seq_0 AAAAAAAAA
seq_1 BBBBBBBBB
seq_2 CCCCCCCCC
"""
f_name = self.tempfile(content=msa)
parser = ClustalParser()
with open(f_name, "r") as f_in:
sequence_file = parser.read(f_in)
for i, sequence_entry in enumerate(sequence_file):
if i == 0:
self.assertEqual("seq_0", sequence_entry.id)
self.assertEqual("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", sequence_entry.seq)
elif i == 1:
self.assertEqual("seq_1", sequence_entry.id)
self.assertEqual("BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB", sequence_entry.seq)
elif i == 2:
self.assertEqual("seq_2", sequence_entry.id)
self.assertEqual("CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC", sequence_entry.seq)
def test_read_1(self):
seq = """CLUSTAL W
seq_0 MLDLEVVPE-RSLGNEQW-------E-F-TLG-MPLAQAV-AILQKHC--
seq_0 -RIIKNVQV
"""
f_name = self.tempfile(content=seq)
parser = ClustalParser()
with open(f_name, "r") as f_in:
sequence_file = parser.read(f_in)
sequence_entry = sequence_file.top_sequence
ref_id = "seq_0"
self.assertEqual(ref_id, sequence_entry.id)
ref_seq = "MLDLEVVPE-RSLGNEQW-------E-F-TLG-MPLAQAV-AILQKHC---RIIKNVQV"
self.assertEqual(ref_seq, sequence_entry.seq)
def test_write_1(self):
seq = [
"CLUSTAL FORMAT written with ConKit",
"",
"seq_0\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"seq_1\tBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB",
"" "seq_0\tAAAAAAAAAAAAAAAAAAAAAA",
"seq_1\tBBBBBBBBBBBBBBBBBBBBBB",
]
joinedseq = "\n".join(seq)
f_name_in = self.tempfile(content=joinedseq)
f_name_out = self.tempfile()
parser = ClustalParser()
with open(f_name_in, "r") as f_in, open(f_name_out, "w") as f_out:
sequence_file = parser.read(f_in)
parser.write(f_out, sequence_file)
with open(f_name_out, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(seq, output)
def test_write_1(self):
seq = [
"CLUSTAL FORMAT written with ConKit",
"",
"seq_0\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"seq_1\tBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB",
""
"seq_0\tAAAAAAAAAAAAAAAAAAAAAA",
"seq_1\tBBBBBBBBBBBBBBBBBBBBBB",
]
joinedseq = '\n'.join(seq)
f_name_in = create_tmp_f(content=joinedseq)
f_name_out = create_tmp_f()
parser = ClustalParser()
with open(f_name_in, 'r') as f_in, open(f_name_out, 'w') as f_out:
sequence_file = parser.read(f_in)
parser.write(f_out, sequence_file)
with open(f_name_out, 'r') as f_in:
output = f_in.read().splitlines()
self.assertEqual(seq, output)
map(os.unlink, [f_name_in, f_name_out])