def raise_error_if_unequal(self, sequence_id: pSeq.SequenceID,
expected_sequence: str,
fasta_provider: FromFile) -> None:
for i, expected_symbol in enumerate(expected_sequence):
expected_base = pNode.Base(expected_symbol)
actual_base = fasta_provider.get_base(sequence_id, i)
self.assertEqual(expected_base, actual_base)
def test_1_one_sequence(self):
fasta_path = self.fasta_dir + "test_1_one_sequence.fasta"
fasta_provider = FromFile(Path(fasta_path))
sequence_id = pSeq.SequenceID("seq1")
expected_sequence = self.read_sequence(fasta_path)
self.raise_error_if_unequal(sequence_id, expected_sequence, fasta_provider)
def test_6_repeated_sequences(self):
fasta_path = self.fasta_dir + "test_6_repeated_sequences.fasta"
with self.assertRaises(Exception) as exp:
_ = FromFile(Path(fasta_path))
expected_message = "Incorrect fasta provided as fasta source. Sequences ids are not unique."
actual_message = str(exp.exception)
self.assertEqual(expected_message, actual_message)
def test_5_empty_fasta(self):
fasta_path = self.fasta_dir + "test_5_empty_fasta.fasta"
with self.assertRaises(Exception) as exp:
_ = FromFile(Path(fasta_path))
expected_message = "No sequences in fasta provided as fasta source or incorrect fasta."
actual_message = str(exp.exception)
self.assertEqual(expected_message, actual_message)
def test_7_no_fasta_in_zip(self):
fasta_path = self.fasta_dir + "test_7_no_fasta_in_zip.zip"
with self.assertRaises(Exception) as exp:
_ = FromFile(Path(fasta_path))
expected_message = "No sequences in zip provided as fasta source or incorrect fastas in zip."
actual_message = str(exp.exception)
self.assertEqual(expected_message, actual_message)
def test_6_empty_zip(self):
fasta_path = self.fasta_dir + "test_6_empty_zip.zip"
with self.assertRaises(Exception) as exp:
_ = FromFile(Path(fasta_path))
expected_message = "Incorrect zip fasta source."
actual_message = str(exp.exception)
self.assertEqual(expected_message, actual_message)
def test_1_one_sequence_one_file_in_zip(self):
fasta_path = self.fasta_dir + "test_1_one_sequence_one_file_in_zip.zip"
fasta_provider = FromFile(Path(fasta_path))
sequence_id = pSeq.SequenceID("seq1")
expected_sequence = "ACTGGGTGGGA"
self.raise_error_if_unequal(sequence_id, expected_sequence,
fasta_provider)
def test_4_empty_sequence(self):
fasta_path = self.fasta_dir + "test_4_empty_sequence.fasta"
with self.assertRaises(Exception) as exp:
_ = FromFile(Path(fasta_path))
expected_message = "Empty sequence in fasta source file. " \
"Provide the sequence or remove its identifier."
actual_message = str(exp.exception)
self.assertEqual(expected_message, actual_message)
def test_2_three_sequences(self):
fasta_path = self.fasta_dir + "test_2_three_sequences.fasta"
fasta_provider = FromFile(Path(fasta_path))
sequence_id_1 = pSeq.SequenceID("seq1")
self.raise_error_if_unequal(sequence_id_1, "ACTGGGTGGGA", fasta_provider)
sequence_id_2 = pSeq.SequenceID("seq2")
self.raise_error_if_unequal(sequence_id_2, "AA", fasta_provider)
sequence_id_3 = pSeq.SequenceID("seq3")
self.raise_error_if_unequal(sequence_id_3, "GT", fasta_provider)