def test_validate_args():
"""Test for existence check for gene expression file.
Test if validation function raises an exception when gene expression file is missing.
"""
with pytest.raises(ArgumentValidateException):
args = parse_args(["mock_filename"])
validate_args(args)
def test_validate_tpm_args(create_expression_files, create_output_files):
"""Test for existence of gene lengths file when TPM normalization type is used."""
expression_path = create_expression_files[0]
tpm_output_path = create_output_files[0]
cmdline = [f"--tpm-output={tpm_output_path}", f"{expression_path}"]
with pytest.raises(ArgumentValidateException):
args = parse_args(cmdline)
validate_args(args)
def test_parse_args():
"""Test argument parser."""
cmdline = [
"--gene-lengths=lengths.tsv", "--cpm-output=expr.cpm.tsv",
"--tpm-output=expr.tpm.tsv", "expr.tsv"
]
args = parse_args(cmdline)
checks = [
args.expression == "expr.tsv",
args.gene_lengths == "lengths.tsv",
args.tpm_output == "expr.tpm.tsv",
args.cpm_output == "expr.cpm.tsv",
]
assert all(checks)
def test_normalization_output_success(create_expression_files,
create_output_files):
"""Test TPM and CPM output.
This test implements the contents of main function and checks if the
normalization outputs are correctly written to files.
"""
expression_path, gene_lengths_path = create_expression_files
tpm_output_path, cpm_output_path = create_output_files
cmdline = [
f"--gene-lengths={gene_lengths_path}",
f"--cpm-output={cpm_output_path}",
f"--tpm-output={tpm_output_path}",
f"{expression_path}",
]
args = parse_args(cmdline)
# Test if validation passes when files exist
validate_args(args)
# Test if tpm and cpm can be computed and written to files
expressions = load_expressions(expression_path)
if cpm_output_path:
CPM = cpm(expressions)
CPM.to_csv(cpm_output_path, sep="\t")
if tpm_output_path:
gene_lengths = load_gene_lengths(gene_lengths_path)
TPM = tpm(expressions, gene_lengths)
TPM.to_csv(tpm_output_path, sep="\t")
# Re-read the values in files and check if they are correct
manually_computed_CPM = [[23809, 20000], [952380, 950000], [23809, 30000]]
CPM = pd.DataFrame(pd.read_csv(cpm_output_path, sep="\t"),
columns=["S1", "S2"])
assert np.all(np.asarray(CPM, dtype=int) == manually_computed_CPM)
manually_computed_TPM = [[20704, 17400], [959266, 957349], [20029, 25250]]
TPM = pd.DataFrame(pd.read_csv(tpm_output_path, sep="\t"),
columns=["S1", "S2"])
assert np.all(np.asarray(TPM, dtype=int) == manually_computed_TPM)