def test_print_ensembl_unknown_resource(mocker, transcripts_handle):
"""Test print ensembl function"""
# GIVEN a temporary directory and some exac lines
build = "37"
tx_file_name = "ensembl_exons_{}.txt".format(build)
tx_lines = [line.strip() for line in transcripts_handle]
mocker.patch("scout.utils.scout_requests.fetch_ensembl_biomart", return_value=tx_lines)
dir_name = tempfile.TemporaryDirectory()
the_dir = pathlib.Path(dir_name.name)
# WHEN fetching and printing the exac data
with pytest.raises(SyntaxError):
print_ensembl(the_dir, resource_type="unknown", genome_build=build)
def test_print_ensembl_exons(mocker, transcripts_handle):
"""Test print ensembl function"""
# GIVEN a temporary directory and some exac lines
build = "37"
tx_file_name = "ensembl_exons_{}.txt".format(build)
tx_lines = [line.strip() for line in transcripts_handle]
mocker.patch("scout.utils.scout_requests.fetch_ensembl_biomart", return_value=tx_lines)
dir_name = tempfile.TemporaryDirectory()
the_dir = pathlib.Path(dir_name.name)
# WHEN fetching and printing the exac data
print_ensembl(the_dir, resource_type="exons", genome_build=build)
i = 0
for i, line in enumerate(open(the_dir / tx_file_name)):
if len(line) > 10 and i > 0:
assert line.split("\t")[1].startswith("ENSG")
# THEN check some lines where produced
assert i > 0