def test_mash_init_wrong_type(self):
with self.assertRaises(TypeError):
mash.Mash("data/test_df_merge1.csv", "data/test_df_merge1.csv")
mash.Mash(self.test_dir / Path("data/fasta_test_data"),
"data/test_df_merge1.csv")
mash.Mash("data/test_df_merge1.csv",
self.test_dir / Path("data/fasta_test_data"))
def test_mash_init_not_dir(self):
with self.assertRaises(ValueError):
mash.Mash(self.test_dir / Path("data/test_df_merge1.csv"),
self.test_dir / Path("data/test_df_merge1.csv"))
mash.Mash(self.test_dir / Path("data/fasta_test_data"),
self.test_dir / Path("data/test_df_merge1.csv"))
mash.Mash(self.test_dir / Path("data/test_df_merge1.csv"),
self.test_dir / Path("data/fasta_test_data"))
def test_mash_init_wrong_path(self):
with self.assertRaises(FileNotFoundError):
mash.Mash(self.test_dir / Path("not_existing"),
self.test_dir / Path("data/fasta_test_data"))
mash.Mash(self.test_dir / Path("data/fasta_test_data"),
self.test_dir / Path("not_existing"))
mash.Mash(self.test_dir / Path("not_existing"),
self.test_dir / Path("not_existing"))
def test_mash_sketches(self):
ws = mash.Mash(self.test_dir / Path("data/fasta_test_data"),
self.test_dir / Path("data/blast_query_data"))
host_s, phage_s = ws.sketch("test_host_s", "test_phage_s")
self.assertTrue(host_s.exists())
self.assertTrue(phage_s.exists())
host_s.unlink()
phage_s.unlink()
def test_mash_predicts(self):
ws = mash.Mash(self.test_dir / Path("data/test_trnascan_host"),
self.test_dir / Path("data/test_trnascan_phage"))
host_s, phage_s = ws.sketch("test_host_s", "test_phage_s")
outfile = ws.run_mash(host_s, phage_s, Path("test_outfile.csv"))
self.assertTrue(outfile.exists())
df = pd.read_table(outfile,
names=("Query", "Target", "Distance", "pval",
"hashes"))
df["Query"] = df["Query"].map(lambda x: x.split("/")[-1].split(".")[0])
df["Target"] = df["Target"].map(
lambda x: x.split("/")[-1].split(".")[0])
df.drop(columns=["hashes"], inplace=True)
outfile.unlink()
self.assertTrue(
df.equals(
pd.DataFrame({
"Query": ["NC_000117|1"],
"Target": ["NC_000902|1"],
"Distance": [1],
"pval": [1]
})))
def test_mash_init_ok(self):
try:
mash.Mash(self.test_dir / Path("data/fasta_test_data"),
self.test_dir / Path("data/blast_query_data"))
except:
self.fail("Init failed with valid args")