def test_kmers_main_kmers_not_found_error(monkeypatch, tmp_path):
counts_out = tmp_path / "kmers.tsv"
class MockArgs:
def __init__(self):
self.fasta = None
self.size = 4
self.kmers = counts_out
self.force = False
self.norm_method = "ilr"
self.norm_output = None
self.embedding_method = "bhsne"
self.embedding_dimensions = 2
self.embedding_output = None
self.pca_dimensions = 3
self.cpus = 1
self.seed = 42
class MockParser:
def add_argument(self, *args, **kwargs):
pass
def parse_args(self):
return MockArgs()
def return_mock_parser(*args, **kwargs):
return MockParser()
monkeypatch.setattr(argparse,
"ArgumentParser",
return_mock_parser,
raising=True)
with pytest.raises(FileNotFoundError):
kmers.main()
def test_kmers_main_not_enough_inputs_error(monkeypatch):
class MockArgs:
def __init__(self):
self.fasta = None
self.size = 4
self.kmers = None
self.force = True
self.norm_method = "am_clr"
self.norm_output = None
self.embedding_method = "bhsne"
self.embedding_dimensions = 2
self.embedding_output = None
self.pca_dimensions = 3
self.cpus = 1
self.seed = 42
class MockParser:
def add_argument(self, *args, **kwargs):
pass
def parse_args(self):
return MockArgs()
def return_mock_parser(*args, **kwargs):
return MockParser()
monkeypatch.setattr(argparse,
"ArgumentParser",
return_mock_parser,
raising=True)
with pytest.raises(ValueError):
kmers.main()
def test_kmers_main_starting_at_fasta(monkeypatch, tmp_path, assembly):
norm_method = "am_clr"
embed_method = "bhsne"
counts_out = tmp_path / "kmers.tsv"
normalized = tmp_path / f"kmers.{norm_method}.tsv"
embedded = tmp_path / f"kmers.{norm_method}.{embed_method}.tsv"
embed_dimensions = 2
class MockArgs:
def __init__(self):
self.fasta = assembly
self.size = 4
self.kmers = counts_out
self.force = True
self.norm_method = norm_method
self.norm_output = normalized
self.embedding_method = embed_method
self.embedding_dimensions = embed_dimensions
self.embedding_output = embedded
self.pca_dimensions = 3
self.cpus = 1
self.seed = 42
class MockParser:
def add_argument(self, *args, **kwargs):
pass
def parse_args(self):
return MockArgs()
def return_mock_parser(*args, **kwargs):
return MockParser()
monkeypatch.setattr(argparse,
"ArgumentParser",
return_mock_parser,
raising=True)
kmers.main()
assert embedded.exists()
df = pd.read_csv(embedded, sep="\t")
assert "contig" in df.columns
assert f"x_{embed_dimensions}" in df.columns
# Make sure we have all of our embedding dimensions and need to account for our contig column
assert embed_dimensions + 1 == df.shape[1]