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