def test_check_ensembl_id():
with TemporaryDirectory() as tmpdir:
seqs = SequenceData([FASTA_PATH],
require_ensembl_ids=True,
cache_directory_path=tmpdir)
with assert_raises(ValueError):
seqs.get("WeirdID")
def test_check_ensembl_id():
with TemporaryDirectory() as tmpdir:
seqs = SequenceData(
FASTA_PATH,
require_ensembl_ids=True,
cache_directory_path=tmpdir)
with assert_raises(ValueError):
seqs.get("WeirdID")
def test_sequence_type():
with TemporaryDirectory() as tmpdir:
seqs_dna = SequenceData([FASTA_PATH], cache_directory_path=tmpdir)
seq = seqs_dna.get("ENSMUST00000138942")
assert seq is not None, \
"Failed to find sequence for ENSMUST00000138942"
assert isinstance(seq, str), \
"Wrong sequence type, expected %s but got %s" % (str, type(seq))
def test_sequence_type():
with TemporaryDirectory() as tmpdir:
seqs_dna = SequenceData(
FASTA_PATH,
cache_directory_path=tmpdir)
seq = seqs_dna.get("ENSMUST00000138942")
assert seq is not None, \
"Failed to find sequence for ENSMUST00000138942"
assert isinstance(seq, str), \
"Wrong sequence type, expected %s but got %s" % (str, type(seq))
def test_clear_cache():
with TemporaryDirectory() as tmpdir:
seqs = SequenceData(FASTA_PATH, cache_directory_path=tmpdir)
assert not seqs._fasta_dictionary, \
"Expected _fasta_dictionary to load lazily"
seqs._load_or_create_fasta_dictionary_pickle()
assert len(seqs._fasta_dictionary) > 0, \
"FASTA dictionary didn't get created"
seqs.clear_cache()
assert not seqs._fasta_dictionary, \
"Expected FASTA dictionary to be empty after clear_cache()"
assert not exists(seqs.fasta_dictionary_pickle_path), \
"Cached pickle file should have been deleted"
seqs._load_or_create_fasta_dictionary_pickle()
assert exists(seqs.fasta_dictionary_pickle_path), \
"Cached pickle file should have been created"
def test_sequence_type():
with TemporaryDirectory() as tmpdir:
seqs_dna = SequenceData(FASTA_PATH,
sequence_type=DNA,
cache_directory_path=tmpdir)
seq = seqs_dna.get("ENSMUST00000138942")
assert isinstance(seq, DNA)
with TemporaryDirectory() as tmpdir:
seqs_str = SequenceData(FASTA_PATH,
sequence_type=str,
cache_directory_path=tmpdir)
seq = seqs_str.get("ENSMUST00000138942")
assert isinstance(seq, str)
def test_clear_cache():
with TemporaryDirectory() as tmpdir:
seqs = SequenceData(FASTA_PATH, cache_directory_path=tmpdir)
assert not seqs._fasta_dictionary, \
"Expected _fasta_dictionary to load lazily"
seqs._load_or_create_fasta_dictionary_pickle()
assert len(seqs._fasta_dictionary) > 0, \
"FASTA dictionary didn't get created"
seqs.clear_cache()
assert not seqs._fasta_dictionary, \
"Expected FASTA dictionary to be empty after clear_cache()"
assert not exists(seqs.fasta_dictionary_pickle_path), \
"Cached pickle file should have been deleted"
seqs._load_or_create_fasta_dictionary_pickle()
assert exists(seqs.fasta_dictionary_pickle_path), \
"Cached pickle file should have been created"
def test_missing_sequence():
with TemporaryDirectory() as tmpdir:
seqs = SequenceData([FASTA_PATH], cache_directory_path=tmpdir)
seq = seqs.get("NotInFasta")
assert seq is None, "Should get None back for missing sequence"
def test_missing_sequence():
with TemporaryDirectory() as tmpdir:
seqs = SequenceData(FASTA_PATH, cache_directory_path=tmpdir)
seq = seqs.get("NotInFasta")
assert seq is None, "Should get None back for missing sequence"