def test_get_dist_matrix(self):
        """Test dnadiff pairwise on multiple bins and get the resulting
        distance matrix"""
        names = [
            "sample0_gt1000_bin0",
            "sample0_gt1000_bin10",
            "sample0_gt1000_bin11",
            "sample0_gt1000_bin1",
            "sample0_gt1000_bin2",
            "sample1_gt1000_bin51",
            "sample1_gt1000_bin67",
            "sample1_gt1000_bin6",
        ]
        files = [ospj(DATA_PATH, "{}.fa".format(n)) for n in names]
        dnadiff_dist_matrix.run_dnadiff_pairwise(files, names,
                TMP_BASENAME_DIR)
        for f in [
            ospj(TMP_BASENAME_DIR,
                "{}_vs_{}".format(names[i], names[j]), "out.report")
                for i in range(len(names))
                for j in range(i + 1, len(names))]:
            ok_(os.path.exists(f))

        matrix = dnadiff_dist_matrix.get_dist_matrix(TMP_BASENAME_DIR, names,
                50)
        matrix_exp = np.genfromtxt(ospj(DATA_PATH, "expected_dist_matrix.tsv"),
                delimiter="\t")
        np.testing.assert_almost_equal(matrix, matrix_exp, decimal=2)
Beispiel #2
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    def test_get_dist_matrix(self):
        """Test dnadiff pairwise on multiple bins and get the resulting
        distance matrix"""
        names = [
            "sample0_gt1000_bin0",
            "sample0_gt1000_bin10",
            "sample0_gt1000_bin11",
            "sample0_gt1000_bin1",
            "sample0_gt1000_bin2",
            "sample1_gt1000_bin51",
            "sample1_gt1000_bin67",
            "sample1_gt1000_bin6",
        ]
        files = [ospj(DATA_PATH, "{}.fa".format(n)) for n in names]
        dnadiff_dist_matrix.run_dnadiff_pairwise(files, names,
                                                 TMP_BASENAME_DIR)
        for f in [
                ospj(TMP_BASENAME_DIR, "{}_vs_{}".format(names[i], names[j]),
                     "out.report") for i in range(len(names))
                for j in range(i + 1, len(names))
        ]:
            ok_(os.path.exists(f))

        matrix = dnadiff_dist_matrix.get_dist_matrix(TMP_BASENAME_DIR, names,
                                                     50)
        matrix_exp = np.genfromtxt(ospj(DATA_PATH, "expected_dist_matrix.tsv"),
                                   delimiter="\t")
        np.testing.assert_almost_equal(matrix, matrix_exp, decimal=2)
 def test_run_dnadiff_pairwise(self):
     """Test dnadiff pairwise on multiple bins"""
     names = ["bin{0}".format(i) for i in range(3)]
     dnadiff_dist_matrix.run_dnadiff_pairwise(
         [ospj(DATA_PATH, b) for b in
             ["sample0_gt1000_bin0.fa", "sample0_gt1000_bin1.fa",
                 "sample0_gt1000_bin2.fa"]],
         names, TMP_BASENAME_DIR)
     for f in [
         ospj(TMP_BASENAME_DIR,
             "{}_vs_{}".format(names[i], names[j]), "out.report")
             for i in range(len(names))
             for j in range(i + 1, len(names))]:
         ok_(os.path.exists(f))
Beispiel #4
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 def test_run_dnadiff_pairwise(self):
     """Test dnadiff pairwise on multiple bins"""
     names = ["bin{0}".format(i) for i in range(3)]
     dnadiff_dist_matrix.run_dnadiff_pairwise([
         ospj(DATA_PATH, b) for b in [
             "sample0_gt1000_bin0.fa", "sample0_gt1000_bin1.fa",
             "sample0_gt1000_bin2.fa"
         ]
     ], names, TMP_BASENAME_DIR)
     for f in [
             ospj(TMP_BASENAME_DIR, "{}_vs_{}".format(names[i], names[j]),
                  "out.report") for i in range(len(names))
             for j in range(i + 1, len(names))
     ]:
         ok_(os.path.exists(f))