def test_csv_report(): with NamedTemporaryFile(mode="r", delete=False) as f: csv_args = cli_args_for_b16_seqdata + ["--output-csv", f.name] run_shell_script(csv_args) contents = f.read() lines = contents.split("\n") assert len(lines) > 0
def test_html_report(): with NamedTemporaryFile(mode="r") as f: html_args = cli_args_for_b16_seqdata + ["--output-html", f.name] run_shell_script(html_args) contents = f.read() lines = contents.split("\n") assert len(lines) > 0
def test_pdf_report(): with NamedTemporaryFile(mode="r") as f: pdf_args = cli_args_for_b16_seqdata + ["--output-pdf-report", f.name] run_shell_script(pdf_args) contents = f.read() # check that something got written - should eventually check that PDF is valid... lines = contents.split("\n") assert len(lines) > 0
def test_report_no_peptides(mock_vaccine_peptides_for_variant): # simulate case where we have no epitopes for any variant mock_vaccine_peptides_for_variant.return_value = [] with NamedTemporaryFile(mode="r") as f: html_args = cli_args_for_b16_seqdata + ["--output-csv", f.name] # test that this doesn't crash and that the CSV output is empty run_shell_script(html_args) contents = f.read() assert contents == ''
def test_ascii_report_real_netmhc_predictor(): with NamedTemporaryFile(mode="r") as f: ascii_args = cli_args_for_b16_seqdata_real_predictor + [ "--output-ascii-report", f.name] run_shell_script(ascii_args) contents = f.read() lines = contents.split("\n") assert len(lines) > 0 no_variants_text = 'No variants' assert no_variants_text not in contents
def test_isovar_csv(): with NamedTemporaryFile(mode="r") as f: isovar_csv_args = cli_args_for_b16_seqdata + [ "--output-isovar-csv", f.name, # TODO: make this flag not necessary "--output-csv", f.name + "ignored" ] run_shell_script(isovar_csv_args) df = pd.read_csv(f) assert len(df) > 1
def test_all_variant_csv_report(): with NamedTemporaryFile(mode="r") as f: all_csv_args = cli_args_for_b16_seqdata + [ "--output-passing-variants-csv", f.name, "--output-csv", f.name + "ignored"] run_shell_script(all_csv_args) contents = f.read() lines = contents.split("\n") assert len(lines) > 0 # make sure it can be a valid dataframe f.seek(0) df = pd.read_csv(f) assert len(df) > 0
def test_all_variant_csv_report(): with NamedTemporaryFile(mode="r") as f: all_csv_args = cli_args_for_b16_seqdata + [ "--output-passing-variants-csv", f.name, # TODO: make this flag not necessary "--output-csv", f.name + "ignored"] run_shell_script(all_csv_args) contents = f.read() lines = contents.split("\n") assert len(lines) > 1 # make sure it can be a valid dataframe f.seek(0) df = pd.read_csv(f) assert len(df) > 1
def test_pdf_report(): with NamedTemporaryFile(mode="rb") as f: pdf_args = cli_args_for_b16_seqdata + ["--output-pdf-report", f.name] run_shell_script(pdf_args) assert getsize(f.name) > 0
def test_xlsx_report(): with NamedTemporaryFile(mode="r") as f: xlsx_args = cli_args_for_b16_seqdata + ["--output-xlsx-report", f.name] run_shell_script(xlsx_args) book = open_workbook(f.name) assert book.nsheets > 0