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(pNode.Base(expected_symbol), actual_base)
def test_2_read_seqeunce_from_cache_instead_downloading(self):
fasta_provider = FromNCBI(EmailAddress('*****@*****.**'), use_cache=True)
cache_dir_path = pathtools.get_child_path(Path.cwd(), ".fastacache")
if cache_dir_path.exists():
shutil.rmtree(cache_dir_path)
cache_dir_path.mkdir()
sequence_id = pSeq.SequenceID("seq1")
fake_sequence = "foo"
expected_base = pNode.Base("o")
fake_fasta_path = pathtools.get_child_path(cache_dir_path,
f"{sequence_id}.fasta")
with open(fake_fasta_path, 'w') as fake_fasta_handler:
fake_fasta_handler.write(f">{sequence_id} cached\n{fake_sequence}")
actual_base = fasta_provider.get_base(sequence_id, 2)
self.assertEqual(expected_base, actual_base)
def bid(x):
return pNode.Base(x)
def b(x):
return pNode.Base(x)