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_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_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_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
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
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
