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 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
def read(self, f_handle, f_id="a2m"): """Read a sequence file Parameters ---------- f_handle Open file handle [read permissions] f_id : str, optional Unique sequence file identifier Returns ------- :obj:`~conkit.core.sequencefile.SequenceFile` """ hierarchy = SequenceFile(f_id) for i, line in enumerate(f_handle): line = line.strip() if line: for j, char in enumerate(line): if char.isalpha() or char == "-": continue indicator = ["-"] * len(line) indicator[j] = "^" msg = "Unknown character in line {0}:{1}{1}{2}{1}{3}" msg = msg.format(i + 1, "\n", line, "".join(indicator)) raise ValueError(msg) sequence = Sequence("seq_{}".format(i), line) hierarchy.add(sequence) return hierarchy
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_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_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_remark_5(self): sequence_file = SequenceFile("test") sequence_file.remark = "hello" sequence = Sequence("foo", "GSMFTPK") sequence.remark = "bar" sequence_file.add(sequence) self.assertEqual(["hello"], sequence_file.remark) self.assertEqual(["bar"], sequence_file[0].remark)
def test_remark_5(self): sequence_file = SequenceFile('test') sequence_file.remark = 'hello' sequence = Sequence('foo', 'GSMFTPK') sequence.remark = 'bar' sequence_file.add(sequence) self.assertEqual(['hello'], sequence_file.remark) self.assertEqual(['bar'], sequence_file[0].remark)
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 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 read(self, f_handle, f_id='fasta'): """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 hierarchy = SequenceFile(f_id) # Read any possible comments and store in file remarks while True: line = f_handle.readline().rstrip() if not line: continue elif line.startswith('#'): hierarchy.remark = line[1:] elif line.startswith('>'): break # Read the sequence record(s) and store them while True: if not line.startswith('>'): raise ValueError("Fasta record needs to start with '>'") id = line[1:] # Header without '>' 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) # Sequence from chunks # Create the sequence record instance sequence_entry = Sequence(id, _seq_string) # Store the sequence in the file hierarchy.add(sequence_entry) if not line: break return hierarchy
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 read(self, f_handle, f_id="fasta"): """Read a sequence file Parameters ---------- f_handle Open file handle [read permissions] f_id : str, optional Unique sequence file identifier Returns ------- :obj:`~conkit.core.sequencefile.SequenceFile` Raises ------ :exc:`ValueError` FASTA record needs to start with > """ hierarchy = SequenceFile(f_id) while True: line = f_handle.readline().rstrip() if not line: continue elif line.startswith("#"): hierarchy.remark = line[1:] elif line.startswith(">"): break while True: if not line.startswith(">"): raise ValueError("Fasta record needs to start with '>'") id = line[1:] # Header without '>' 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) # Sequence from chunks sequence_entry = Sequence(id, _seq_string) hierarchy.add(sequence_entry) if not line: break return hierarchy
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_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_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_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_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_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_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_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_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_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_6(self): sequence_file = SequenceFile('test') for s in [ Sequence('foo', 'AAAAAAA'), Sequence('bar', 'AA-ABA-'), Sequence('cho', 'AAACBAA'), Sequence('doo', 'B-BAA--'), Sequence('miu', 'BBBBBBB'), Sequence('nop', 'AAAAAAB') ]: sequence_file.add(s) self.assertEqual(5, sequence_file.neff)
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_get_weights_6(self): sequence_file = SequenceFile('test') for s in [ Sequence('foo', 'AAAAAAA'), Sequence('bar', 'AA-ACA-'), Sequence('cho', 'AAADCAA'), Sequence('doo', 'C-CAA--'), Sequence('miu', 'CCCCCCC'), Sequence('nop', 'AAAAAAB') ]: sequence_file.add(s) self.assertEqual(5, sequence_file.meff)
def test_get_weights_6(self): sequence_file = SequenceFile("test") for s in [ Sequence("foo", "AAAAAAA"), Sequence("bar", "AA-ACA-"), Sequence("cho", "AAADCAA"), Sequence("doo", "C-CAA--"), Sequence("miu", "CCCCCCC"), Sequence("nop", "AAAAAAB"), ]: sequence_file.add(s) self.assertEqual(5, sequence_file.meff)
def test_get_weights_6(self): sequence_file = SequenceFile("test") for s in [ Sequence("foo", "AAAAAAA"), Sequence("bar", "AA-ACA-"), Sequence("cho", "AAADCAA"), Sequence("doo", "C-CAA--"), Sequence("miu", "CCCCCCC"), Sequence("nop", "AAAAAAB"), ]: sequence_file.add(s) weights = sequence_file.get_weights(identity=0.6) self.assertEqual(weights, [0.3333333333333333, 1.0, 0.5, 1.0, 1.0, 0.5])