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"""
Test SequenceData object to make sure it's correctly parsing FASTA files
and that we're able to clear and regenrate its cached representation of
a FASTA dictionary
"""
from os.path import exists
from pyensembl import SequenceData
from .common import TemporaryDirectory
from .data import data_path
FASTA_PATH = data_path("mouse.ensembl.81.partial.ENSMUSG00000017167.fa")
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_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_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()"
for pickle_path in seqs.fasta_dictionary_pickle_paths:
assert not exists(
pickle_path
), "Cached pickle file should have been deleted"
seqs._load_or_create_fasta_dictionary_pickle()
for pickle_path in seqs.fasta_dictionary_pickle_paths:
assert exists(pickle_path), "Cached pickle file should have been created"
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