Example #1
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 def test_newick_to_tree_node_convert_underscores(self):
     fh = StringIO('(_:0.1, _a, _b)__;')
     tree = _newick_to_tree_node(fh, convert_underscores=False)
     fh2 = StringIO()
     _tree_node_to_newick(tree, fh2)
     self.assertEqual(fh2.getvalue(), "('_':0.1,'_a','_b')'__';\n")
     fh2.close()
     fh.close()
Example #2
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 def test_newick_to_tree_node_invalid_files(self):
     for invalid, error_fragments in self.invalid_newicks:
         fh = StringIO(invalid)
         with self.assertRaises(NewickFormatError) as cm:
             _newick_to_tree_node(fh)
         for frag in error_fragments:
             self.assertIn(frag, str(cm.exception))
         fh.close()
Example #3
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    def test_tree_node_to_newick(self):
        for tree, newicks in self.trees_newick_lists:
            newick = newicks[0]
            fh = StringIO()
            _tree_node_to_newick(tree, fh)

            self.assertEqual(newick, fh.getvalue())

            fh.close()
Example #4
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    def test_newick_to_tree_node_valid_files(self):
        for tree, newicks in self.trees_newick_lists:
            for newick in newicks:
                fh = StringIO(newick)
                read_tree = _newick_to_tree_node(fh)

                self._assert_equal(tree, read_tree)

                fh.close()
Example #5
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    def test_roundtrip(self):
        for tree, newicks in self.trees_newick_lists:
            newick = newicks[0]
            fh = StringIO(newick)
            tree = _newick_to_tree_node(fh)
            fh2 = StringIO()
            _tree_node_to_newick(tree, fh2)
            fh2.seek(0)
            tree2 = _newick_to_tree_node(fh2)

            self.assertEqual(newick, fh2.getvalue())
            self._assert_equal(tree, tree2)

            fh.close()
            fh2.close()
Example #6
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    def test_roundtrip_read_write(self):
        for reader_fn, writer_fn, fhs in (
            (_lsmat_to_dissimilarity_matrix, _dissimilarity_matrix_to_lsmat, self.dissim_fhs),
            (_lsmat_to_distance_matrix, _distance_matrix_to_lsmat, self.dist_fhs),
        ):
            for fh in fhs:
                # Read.
                fh.seek(0)
                lsmat1 = reader_fn(fh)

                # Write.
                out_fh = StringIO()
                writer_fn(lsmat1, out_fh)
                out_fh.seek(0)

                # Read.
                lsmat2 = reader_fn(out_fh)
                out_fh.close()

                self.assertEqual(lsmat1, lsmat2)
Example #7
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    def test_write(self):
        for fn, objs, strs in ((_dissimilarity_matrix_to_lsmat,
                                self.dissim_objs, self.dissim_strs),
                               (_distance_matrix_to_lsmat, self.dist_objs,
                                self.dist_strs)):
            for obj, str_ in zip(objs, strs):
                fh = StringIO()
                fn(obj, fh)
                obs = fh.getvalue()
                fh.close()
                self.assertEqual(obs, str_)

        # Test writing CSV (TSV is written above).
        for fn, cls in ((_dissimilarity_matrix_to_lsmat, DissimilarityMatrix),
                        (_distance_matrix_to_lsmat, DistanceMatrix)):
            obj = cls(self.lsmat_3x3_data, ['a', 'b', 'c'])
            fh = StringIO()
            fn(obj, fh, delimiter=',')
            obs = fh.getvalue()
            fh.close()
            self.assertEqual(obs, LSMat_3x3_CSV)
Example #8
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    def test_roundtrip_read_write(self):
        for reader_fn, writer_fn, fhs in ((_lsmat_to_dissimilarity_matrix,
                                           _dissimilarity_matrix_to_lsmat,
                                           self.dissim_fhs),
                                          (_lsmat_to_distance_matrix,
                                           _distance_matrix_to_lsmat,
                                           self.dist_fhs)):
            for fh in fhs:
                # Read.
                fh.seek(0)
                lsmat1 = reader_fn(fh)

                # Write.
                out_fh = StringIO()
                writer_fn(lsmat1, out_fh)
                out_fh.seek(0)

                # Read.
                lsmat2 = reader_fn(out_fh)
                out_fh.close()

                self.assertEqual(lsmat1, lsmat2)
Example #9
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    def test_write(self):
        for fn, objs, strs in (
            (_dissimilarity_matrix_to_lsmat, self.dissim_objs, self.dissim_strs),
            (_distance_matrix_to_lsmat, self.dist_objs, self.dist_strs),
        ):
            for obj, str_ in zip(objs, strs):
                fh = StringIO()
                fn(obj, fh)
                obs = fh.getvalue()
                fh.close()
                self.assertEqual(obs, str_)

        # Test writing CSV (TSV is written above).
        for fn, cls in (
            (_dissimilarity_matrix_to_lsmat, DissimilarityMatrix),
            (_distance_matrix_to_lsmat, DistanceMatrix),
        ):
            obj = cls(self.lsmat_3x3_data, ["a", "b", "c"])
            fh = StringIO()
            fn(obj, fh, delimiter=",")
            obs = fh.getvalue()
            fh.close()
            self.assertEqual(obs, LSMat_3x3_CSV)
Example #10
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 def test_newick_sniffer_invalid_files(self):
     for invalid, _ in self.invalid_newicks:
         fh = StringIO(invalid)
         self.assertEqual(_newick_sniffer(fh), (False, {}))
         fh.close()
Example #11
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 def test_newick_sniffer_valid_files(self):
     for _, newicks in self.trees_newick_lists:
         for newick in newicks:
             fh = StringIO(newick)
             self.assertEqual(_newick_sniffer(fh), (True, {}))
             fh.close()