def test_top_sequence_3(self):
sequence_file = SequenceFile("test")
sequence1 = Sequence("foo", "AAAAA")
sequence2 = Sequence("bar", "CCCCC")
sequence_file.add(sequence1)
sequence_file.add(sequence2)
self.assertEqual(sequence1, sequence_file.top_sequence)
def test_align_local_3(self):
sequence1 = Sequence(
'foo', '------------------------------------------'
'------------------------------------------'
'----------W------------TV-----------------'
'---F--C----AM---GLD-----------C--KFE-NF---'
'----N-D-----G---------C-D----G--NLC-IP----'
'----I--------------NG--------------D----IR'
'GC-')
sequence2 = Sequence(
'bar', '-D-------------------------------GGTYTP---'
'-------------C-PHDCGS-R-------------------'
'------------------------------TG--EN------'
'-KV------------------------------KFESN-N-Q'
'ATNR------D----Q--------------------------'
'------------------------WVA--NR-----------'
'---')
sequence1.align_local(sequence2,
id_chars=2,
nonid_chars=1,
gap_open_pen=-1.0,
gap_ext_pen=-0.5,
inplace=True)
aligned1 = "---------------------------------------------------------------------------" \
"-------------------W------------TV--------------------F--C----AM---GLD-----" \
"------C--KFE-NF-------N-D-----G---------C-D----G--NLC-IP--------I----------" \
"----NG--------------D----IRGC-"
aligned2 = "-D-------------------------------GGTYTP----------------C-PHDCGS-R----------" \
"---------------------------------------TG--EN-------KV---------------------" \
"---------KFESN-N-QATNR------D----Q-----------------------------------------" \
"---------WVA--NR--------------"
self.assertEqual(aligned1, sequence1.seq)
self.assertEqual(aligned2, sequence2.seq)
def test_align_local_2(self):
sequence1 = Sequence(
'foo', 'DDLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTV'
'TLGDETYQVMSACKPHDCGSQRIAVMWSEKSNQMTGLFSTIDE'
'KTSQEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNFKV'
'FGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNR'
'NTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDI'
'TASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCR')
sequence2 = Sequence(
'bar', '-------------------------------------------'
'-------------------------------------------'
'--------W------------TV--------------------'
'F--C----AM---GLD-----------C--KFE-NF-------'
'N-D-----G---------C-D----G--NLC-IP--------I'
'--------------NG--------------D----IRGC-')
sequence1.align_local(sequence2,
id_chars=2,
nonid_chars=1,
gap_open_pen=-0.5,
gap_ext_pen=-0.2,
inplace=True)
aligned1 = "DDLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTLGDETYQVMSACKPHDCGSQRIAVMWSEKSN" \
"QMTGLFSTIDEKTSQEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNFKVFGRCELAAAMKRHGLDNYRGY" \
"SLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKI" \
"VSDGNGMNAWVAWRNRCKGTDVQAWIRGCR"
aligned2 = "---------------------------------------------------------------------------" \
"-------------------W------------TV--------------------F--C----AM---GLD-----" \
"------C--KFE-NF-------N-D-----G---------C-D----G--NLC-IP--------I----------" \
"----NG--------------D----IRGC-"
self.assertEqual(aligned1, sequence1.seq)
self.assertEqual(aligned2, sequence2.seq)
def test_top_sequence_3(self):
sequence_file = SequenceFile('test')
sequence1 = Sequence('foo', 'AAAAA')
sequence2 = Sequence('bar', 'CCCCC')
sequence_file.add(sequence1)
sequence_file.add(sequence2)
self.assertEqual(sequence1, sequence_file.top_sequence)
def test_trim_2(self):
sequence_file = SequenceFile("test")
for seq in [Sequence("foo", "AAAAA"), Sequence("bar", "CCCCC"), Sequence("doe", "DDDDD")]:
sequence_file.add(seq)
sequence_file_trimmed = sequence_file.trim(3, 5)
self.assertEqual(["foo", "bar", "doe"], [s.id for s in sequence_file_trimmed])
self.assertEqual(["AAA", "CCC", "DDD"], [s.seq for s in sequence_file_trimmed])
self.assertNotEqual(sequence_file, sequence_file_trimmed)
def test_sort_4(self):
sequence_file = SequenceFile("test")
for seq in [Sequence("foo", "AAAAA"), Sequence("bar", "DDDDD"), Sequence("doe", "CCCCC")]:
sequence_file.add(seq)
sequence_file_sorted = sequence_file.sort("seq", reverse=True, inplace=True)
self.assertEqual(["bar", "doe", "foo"], [s.id for s in sequence_file_sorted])
self.assertEqual(["DDDDD", "CCCCC", "AAAAA"], [s.seq for s in sequence_file_sorted])
self.assertEqual(sequence_file, sequence_file_sorted)
def test_ascii_matrix_1(self):
sequence_file = SequenceFile("test")
for seq in [Sequence("foo", "AAAAAA"), Sequence("bar", "-CC-C-"), Sequence("doe", "DDDDDD")]:
sequence_file.add(seq)
matrix = sequence_file.ascii_matrix
self.assertEqual([65, 65, 65, 65, 65, 65], list(matrix)[0])
self.assertEqual([45, 67, 67, 45, 67, 45], list(matrix)[1])
self.assertEqual([68, 68, 68, 68, 68, 68], list(matrix)[2])
def test_trim_4(self):
sequence_file = SequenceFile("test")
for seq in [Sequence("foo", "ACDEF"), Sequence("bar", "CDEFG"), Sequence("doe", "DEFGH")]:
sequence_file.add(seq)
sequence_file_trimmed = sequence_file.trim(2, 3)
self.assertEqual(["foo", "bar", "doe"], [s.id for s in sequence_file_trimmed])
self.assertEqual(["CD", "DE", "EF"], [s.seq for s in sequence_file_trimmed])
self.assertNotEqual(sequence_file, sequence_file_trimmed)
def read(self, f_handle, f_id='stockholm'):
"""Read a sequence file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique sequence file identifier
Returns
-------
:obj:`SequenceFile <conkit.core.sequencefile.SequenceFile>`
"""
# Create a new sequence file instance
sequence_file = SequenceFile(f_id)
# Read any possible comments and store in file remarks
while True:
line = f_handle.readline().rstrip()
if not line:
continue
elif V_RECORD.match(line):
_ = V_RECORD.match(line).group(1)
# sequence_file.add_remark(version)
elif GF_RECORD.match(line) or GS_RECORD.match(line):
break
# Read the sequence record(s)
while True:
if GF_RECORD.match(line):
ident = GF_RECORD.match(line).group(1)[:-3]
sequence_entry = Sequence(ident, "")
sequence_file.add(sequence_entry)
elif GS_RECORD.match(line):
ident, _, desc = GS_RECORD.match(line).groups()
sequence_entry = Sequence(ident, "")
sequence_entry.remark = desc
sequence_file.add(sequence_entry)
elif GR_RECORD.match(line):
pass
elif len(line.split()) == 2 and line.split()[0] in sequence_file:
ident, seq = line.replace('.', '-').split()
sequence_file[ident].seq = sequence_file[ident].seq + seq
line = f_handle.readline().rstrip()
# // char in alignment reached
if END_RECORD.match(line):
break
return sequence_file
def test_diversity_2(self):
sequence_file = SequenceFile('test')
for seq in [
Sequence('foo', 'AAAAAA'),
Sequence('bar', 'AAAAAA'),
Sequence('doe', 'AAAAAA')
]:
sequence_file.add(seq)
self.assertEqual(0.289, sequence_file.diversity)
def test_get_frequency_2(self):
sequence_file = SequenceFile('test')
for s in [
Sequence('foo', '-------'),
Sequence('bar', '-------'),
Sequence('cho', '-------')
]:
sequence_file.add(s)
self.assertEqual([3, 3, 3, 3, 3, 3, 3],
sequence_file.get_frequency("-"))
def test_diversity_4(self):
sequence_file = SequenceFile('test')
for seq in [
Sequence('foo', 'AAAAAA'),
Sequence('bar', 'B'),
Sequence('doe', 'CCC')
]:
sequence_file.add(seq)
with self.assertRaises(ValueError):
sequence_file.diversity
def test_get_frequency_1(self):
sequence_file = SequenceFile('test')
for s in [
Sequence('foo', 'AAAAAAA'),
Sequence('bar', 'A-AAAA-'),
Sequence('cho', '--AAA--')
]:
sequence_file.add(s)
self.assertEqual([1, 2, 0, 0, 0, 1, 2],
sequence_file.get_frequency("X"))
def test_get_frequency_3(self):
sequence_file = SequenceFile('test')
for s in [
Sequence('foo', 'AAAAAAA'),
Sequence('bar', 'AAAAAAA'),
Sequence('cho', 'AAAAAAA')
]:
sequence_file.add(s)
self.assertEqual([0, 0, 0, 0, 0, 0, 0],
sequence_file.get_frequency("X"))
def test_filter_6(self):
sequence_file = SequenceFile('test')
for seq in [
Sequence('foo', 'AAAAAA'),
Sequence('bar', 'AACCCC'),
Sequence('doe', 'DDDDDD')
]:
sequence_file.add(seq)
filtered = sequence_file.filter(min_id=0.1, max_id=0.9)
self.assertEqual(['foo', 'bar'], [s.id for s in filtered])
def test_get_weights_5(self):
sequence_file = SequenceFile("test")
for s in [
Sequence("foo", "AAAAAAA"),
Sequence("bar", "AA-ACA-"),
Sequence("cho", "C-CAA--"),
Sequence("baz", "CCCCCCC"),
]:
sequence_file.add(s)
weights = sequence_file.get_weights(identity=0.6)
self.assertEqual(weights, [1.0, 1.0, 1.0, 1.0])
def test_get_weights_5(self):
sequence_file = SequenceFile('test')
for s in [
Sequence('foo', 'AAAAAAA'),
Sequence('bar', 'AA-ACA-'),
Sequence('cho', 'C-CAA--'),
Sequence('baz', 'CCCCCCC')
]:
sequence_file.add(s)
weights = sequence_file.get_weights(identity=0.6)
self.assertEqual(weights, [1.0, 1.0, 1.0, 1.0])
def test_calculate_weights_5(self):
sequence_file = SequenceFile('test')
for s in [
Sequence('foo', 'AAAAAAA'),
Sequence('bar', 'AA-ABA-'),
Sequence('cho', 'B-BAA--'),
Sequence('baz', 'BBBBBBB')
]:
sequence_file.add(s)
weights = sequence_file.calculate_weights(identity=0.6)
self.assertEqual(weights, [1.0, 1.0, 1.0, 1.0])
def test_get_weights_2(self):
sequence_file = SequenceFile("test")
for s in [
Sequence("foo", "AAAAAAA"),
Sequence("bar", "AAAAAAA"),
Sequence("cho", "AAAAAAA"),
Sequence("baz", "CCCCCCC"),
]:
sequence_file.add(s)
weights = sequence_file.get_weights(identity=0.7)
self.assertEqual(weights, [0.3333333333333333, 0.3333333333333333, 0.3333333333333333, 1.0])
def test_get_weights_1(self):
sequence_file = SequenceFile('test')
for s in [
Sequence('foo', 'AAAAAAA'),
Sequence('bar', 'AAAAAAA'),
Sequence('cho', 'AAAAAAA'),
Sequence('baz', 'AAAAAAA')
]:
sequence_file.add(s)
weights = sequence_file.get_weights(identity=0.7)
self.assertEqual(weights, [0.25, 0.25, 0.25, 0.25])
def test_calculate_freq_3(self):
sequence_file = SequenceFile('test')
for s in [
Sequence('foo', 'AAAAAAA'),
Sequence('bar', 'AAAAAAA'),
Sequence('cho', 'AAAAAAA')
]:
sequence_file.add(s)
calculated_freqs = [
round(i, 6) for i in sequence_file.calculate_freq()
]
self.assertEqual([1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], calculated_freqs)
def test_ascii_matrix_1(self):
sequence_file = SequenceFile('test')
for seq in [
Sequence('foo', 'AAAAAA'),
Sequence('bar', '-CC-C-'),
Sequence('doe', 'DDDDDD')
]:
sequence_file.add(seq)
matrix = sequence_file.ascii_matrix
self.assertEqual([65, 65, 65, 65, 65, 65], list(matrix)[0])
self.assertEqual([45, 67, 67, 45, 67, 45], list(matrix)[1])
self.assertEqual([68, 68, 68, 68, 68, 68], list(matrix)[2])
def test_calculate_weights_2(self):
sequence_file = SequenceFile('test')
for s in [
Sequence('foo', 'AAAAAAA'),
Sequence('bar', 'AAAAAAA'),
Sequence('cho', 'AAAAAAA'),
Sequence('baz', 'BBBBBBB')
]:
sequence_file.add(s)
weights = sequence_file.calculate_weights(identity=0.7)
self.assertEqual(
weights,
[0.3333333333333333, 0.3333333333333333, 0.3333333333333333, 1.0])
def test_calculate_freq_1(self):
sequence_file = SequenceFile('test')
for s in [
Sequence('foo', 'AAAAAAA'),
Sequence('bar', 'A-AAAA-'),
Sequence('cho', '--AAA--')
]:
sequence_file.add(s)
calculated_freqs = [
round(i, 6) for i in sequence_file.calculate_freq()
]
self.assertEqual(
[0.666667, 0.333333, 1.0, 1.0, 1.0, 0.666667, 0.333333],
calculated_freqs)
def test_trim_4(self):
sequence_file = SequenceFile('test')
for seq in [
Sequence('foo', 'ACDEF'),
Sequence('bar', 'CDEFG'),
Sequence('doe', 'DEFGH')
]:
sequence_file.add(seq)
sequence_file_trimmed = sequence_file.trim(2, 3)
self.assertEqual(['foo', 'bar', 'doe'],
[s.id for s in sequence_file_trimmed])
self.assertEqual(['CD', 'DE', 'EF'],
[s.seq for s in sequence_file_trimmed])
self.assertNotEqual(sequence_file, sequence_file_trimmed)
def test_trim_2(self):
sequence_file = SequenceFile('test')
for seq in [
Sequence('foo', 'AAAAA'),
Sequence('bar', 'CCCCC'),
Sequence('doe', 'DDDDD')
]:
sequence_file.add(seq)
sequence_file_trimmed = sequence_file.trim(3, 5)
self.assertEqual(['foo', 'bar', 'doe'],
[s.id for s in sequence_file_trimmed])
self.assertEqual(['AAA', 'CCC', 'DDD'],
[s.seq for s in sequence_file_trimmed])
self.assertNotEqual(sequence_file, sequence_file_trimmed)
def test_write_1(self):
contact_file = ContactFile("RR")
contact_file.target = "R9999"
contact_file.author = "1234-5678-9000"
contact_file.remark = ["Predictor remarks"]
contact_file.method = ["Description of methods used", "Description of methods used"]
contact_map = ContactMap("1")
contact_file.add(contact_map)
for c in [(1, 9, 0, 8, 0.7), (1, 10, 0, 8, 0.7), (2, 8, 0, 8, 0.9), (3, 12, 0, 8, 0.4)]:
contact = Contact(c[0], c[1], c[4], distance_bound=(c[2], c[3]))
contact_map.add(contact)
contact_map.sequence = Sequence("1", "HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD")
contact_map.set_sequence_register()
f_name = self.tempfile()
with open(f_name, "w") as f_out:
MemBrainParser().write(f_out, contact_file)
content = [
"Helix Position Residue Helix Position Residue Probability",
"Hx 1 H Hx 9 L 0.700000",
"Hx 1 H Hx 10 L 0.700000",
"Hx 2 L Hx 8 I 0.900000",
"Hx 3 E Hx 12 K 0.400000",
]
with open(f_name, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
def test_write_1(self):
contact_file = ContactFile('RR')
contact_file.target = 'R9999'
contact_file.author = '1234-5678-9000'
contact_file.remark = ['Predictor remarks']
contact_file.method = ['Description of methods used', 'Description of methods used']
contact_map = ContactMap('1')
contact_file.add(contact_map)
for c in [(1, 9, 0, 8, 0.7), (1, 10, 0, 8, 0.7), (2, 8, 0, 8, 0.9), (3, 12, 0, 8, 0.4)]:
contact = Contact(c[0], c[1], c[4], distance_bound=(c[2], c[3]))
contact_map.add(contact)
contact_map.sequence = Sequence('1', 'HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD')
contact_map.assign_sequence_register()
f_name = create_tmp_f()
with open(f_name, 'w') as f_out:
PsicovParser().write(f_out, contact_file)
content = [
"1 9 0 8 0.700000",
"1 10 0 8 0.700000",
"2 8 0 8 0.900000",
"3 12 0 8 0.400000",
"",
]
content = os.linesep.join(content)
with open(f_name, 'r') as f_in:
data = "".join(f_in.readlines())
self.assertEqual(content, data)
os.unlink(f_name)
def test_write_1(self):
contact_file = ContactFile("test")
contact_map = ContactMap("1")
contact_file.add(contact_map)
for c in [(1, 9, 0, 8, 0.7), (1, 10, 0, 8, 0.7), (2, 8, 0, 8, 0.9),
(3, 12, 0, 8, 0.4)]:
contact = Contact(c[0], c[1], c[4], distance_bound=(c[2], c[3]))
contact_map.add(contact)
contact_map.sequence = Sequence(
"1",
"HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD"
)
f_name = self.tempfile()
# Not sure if bug in Python3 numpy or intended purpose [Implemented: 21.11.2016]
mode = "wb" if sys.version_info.major == 3 else "w"
with open(f_name, mode) as f_out:
CCMpredParser().write(f_out, contact_file)
content = [
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t6.999999999999999556e-01\t6.999999999999999556e-01\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t9.000000000000000222e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t4.000000000000000222e-01",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t9.000000000000000222e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"6.999999999999999556e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"6.999999999999999556e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t4.000000000000000222e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
]
with open(f_name, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
def read(self, f_handle, f_id='a3m', remove_inserts=True):
"""Read a sequence file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique sequence file identifier
remove_inserts : bool, optional
Remove insert states [default: True]
Returns
-------
:obj:`~conkit.core.sequencefile.SequenceFile`
"""
sequence_file = SequenceFile(f_id)
while True:
line = f_handle.readline().rstrip()
if not line:
continue
elif line.startswith('#'):
sequence_file.remark = line[1:]
elif line.startswith('>'):
break
while True:
if not line.startswith('>'):
raise ValueError("Fasta record needs to start with '>'")
id = line[1:]
chunks = []
line = f_handle.readline().rstrip()
while True:
if not line:
break
elif line.startswith('>'):
break
chunks.append(line)
line = f_handle.readline().rstrip()
seq_string = "".join(chunks)
if remove_inserts:
seq_string = self._remove_inserts(seq_string)
sequence_entry = Sequence(id, seq_string)
try:
sequence_file.add(sequence_entry)
except ValueError:
while True:
new_id = sequence_entry.id + "_{0}".format(
np.random.randint(0, 100000))
if new_id in sequence_file:
continue
else:
break
sequence_entry.id = new_id
sequence_file.add(sequence_entry)
if not line:
break
if not remove_inserts:
self._adjust_insert(sequence_file)
return sequence_file
