How to use the snps.SNPsCollection function in snps

def test_save_discrepant_genotypes(self):
        sc = SNPsCollection()
        sc.load_snps(["tests/input/NCBI36.csv", "tests/input/GRCh37.csv"])
        self.assertEqual(len(sc.discrepant_genotypes), 1)
        discrepant_genotypes_file = sc.save_discrepant_genotypes()
        self.assertEqual(
            os.path.relpath(discrepant_genotypes_file),
            "output/discrepant_genotypes.csv",
        )
        self.assertTrue(os.path.exists(discrepant_genotypes_file))

def test_load_snps_None(self):
        sc = SNPsCollection()
        with self.assertRaises(TypeError):
            sc.load_snps(None)

"discrepant_genotype": bool,
                },
            )

            df1 = df[["chrom", "pos_file1", "genotype_file1"]]
            df2 = df[["chrom", "pos_file2", "genotype_file2"]]

            df1.to_csv(
                dest1, na_rep="--", header=["chromosome", "position", "genotype"]
            )

            df2.to_csv(
                dest2, na_rep="--", header=["chromosome", "position", "genotype"]
            )

            sc = SNPsCollection([dest1, dest2])

            expected = df[
                [
                    "chrom",
                    "discrepant_position",
                    "discrepant_genotype",
                    "expected_position",
                    "expected_genotype",
                ]
            ]
            expected = expected.rename(
                columns={"expected_position": "pos", "expected_genotype": "genotype"}
            )
            expected_snps = SNPs()
            expected_snps._snps = expected
            expected_snps.sort_snps()

def test_save_discrepant_snps_no_discrepant_snps(self):
        sc = SNPsCollection()
        self.assertEqual(len(sc.discrepant_snps), 0)
        self.assertFalse(sc.save_discrepant_snps())

def test_load_snps_non_existent_file(self):
        sc = SNPsCollection()
        sc.load_snps(["tests/input/GRCh37.csv", "tests/input/non_existent_file.csv"])
        pd.testing.assert_frame_equal(sc.snps, self.snps_GRCh37(), check_exact=True)

def test_save_discrepant_genotypes_no_discrepant_snps(self):
        sc = SNPsCollection()
        self.assertEqual(len(sc.discrepant_genotypes), 0)
        self.assertFalse(sc.save_discrepant_genotypes())

def test_load_snps_assembly_mismatch_save_output(self):
        sc = SNPsCollection()
        sc.load_snps(
            ["tests/input/NCBI36.csv", "tests/input/GRCh37.csv"], save_output=True
        )
        self.assertTrue(os.path.exists("output/discrepant_positions_1.csv"))
        self.assertTrue(os.path.exists("output/discrepant_genotypes_1.csv"))
        self.assertEqual(len(sc.discrepant_positions), 4)
        self.assertEqual(len(sc.discrepant_genotypes), 1)
        pd.testing.assert_frame_equal(
            sc.snps, self.snps_NCBI36_discrepant_snps(), check_exact=True
        )

def test_load_snps_assembly_mismatch_exceed_discrepant_positions_threshold(self):
        sc = SNPsCollection()
        sc.load_snps(
            ["tests/input/NCBI36.csv", "tests/input/GRCh37.csv"],
            discrepant_snp_positions_threshold=0,
        )
        self.assertFalse(os.path.exists("output/discrepant_positions_1.csv"))
        self.assertFalse(os.path.exists("output/discrepant_genotypes_1.csv"))
        self.assertEqual(len(sc.discrepant_positions), 4)
        self.assertEqual(len(sc.discrepant_genotypes), 0)
        pd.testing.assert_frame_equal(sc.snps, self.snps_NCBI36(), check_exact=True)

def test_load_snps_assembly_mismatch(self):
        sc = SNPsCollection()
        sc.load_snps(["tests/input/NCBI36.csv", "tests/input/GRCh37.csv"])
        self.assertFalse(os.path.exists("output/ind_discrepant_positions_1.csv"))
        self.assertFalse(os.path.exists("output/ind_discrepant_genotypes_1.csv"))
        self.assertEqual(len(sc.discrepant_positions), 4)
        self.assertEqual(len(sc.discrepant_genotypes), 1)
        pd.testing.assert_frame_equal(
            sc.snps, self.snps_NCBI36_discrepant_snps(), check_exact=True
        )

def test_source_lineage_file_gzip(self):
        sc = SNPsCollection("tests/input/GRCh37.csv")
        self.assertEqual(sc.source, "generic")
        sc.load_snps("tests/input/23andme.txt")
        self.assertEqual(sc.source, "generic, 23andMe")
        file = sc.save_snps()
        with open(file, "rb") as f_in:
            with atomic_write(file + ".gz", mode="wb", overwrite=True) as f_out:
                with gzip.open(f_out, "wb") as f_gzip:
                    shutil.copyfileobj(f_in, f_gzip)
        s = SNPs(file + ".gz")
        self.assertEqual(s.source, "generic, 23andMe")
        pd.testing.assert_frame_equal(sc.snps, s.snps, check_exact=True)