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