add test cases graft level and newick foundation

ghosttree/scaffold/hybridtree.py

@@ -73,10 +73,10 @@ def extensions_onto_foundation(otu_file_fh, extension_taxonomy_fh,
            type '--stderr')
     """
     global foundation_accession_genus_dic  # needs global assignment for flake8
+
     foundation_accession_genus_dic = {}
-    graft_letter = graft_level
-    graft_level_map = {'p': 2, 'c': 3, 'o': 4, 'f': 5, 'g': 6}
-    graft_level = graft_level_map[graft_letter]
+
+    graft_level, graft_letter = _graft_functions(graft_level)
 
     process = subprocess.Popen("muscle", shell=True, stdout=subprocess.PIPE,
                                stderr=subprocess.PIPE)
@@ -332,3 +332,11 @@ def _collapse(tax, level):
     tax = [x.strip() for x in tax.split(';')]
     taxa = tax[:level][-1].split('__')[1].capitalize()
     return taxa
+
+
+def _graft_functions(graft_level):
+    print(graft_level)
+    graft_letter = graft_level
+    graft_level_map = {'p': 2, 'c': 3, 'o': 4, 'f': 5, 'g': 6}
+    graft_level = graft_level_map[graft_letter]
+    return graft_level, graft_letter

ghosttree/scaffold/tests/test_hybridtree.py

@@ -13,6 +13,8 @@
 from skbio import Sequence
 
 from ghosttree.scaffold.hybridtree import _make_nr_foundation_alignment
+from ghosttree.scaffold.hybridtree import _graft_functions
+from ghosttree.scaffold.hybridtree import _make_nr_foundation_newick
 from ghosttree.scaffold.hybridtree import _create_taxonomy_dict
 from ghosttree.scaffold.hybridtree import _make_mini_otu_files
 from ghosttree.scaffold.hybridtree import _extension_genus_accession_dict
@@ -55,11 +57,18 @@ def test_make_nr_foundation_alignment_none(self):
                                                self.graft_letter_g)
         self.assertEqual(list(result), [])
 
-    # def test_newick_file_few_extensions(self):
-    #     result = _make_nr_foundation_newick(self.foundation_newick,
-    #                                         self.extension_genus_dic_few)
-    #
-    #     print('result', result)
+    def test_newick_file_few_extensions(self):
+        result = _make_nr_foundation_newick(self.foundation_newick,
+                                            self.extension_genus_dic_few,
+                                            self.graft_letter_g,
+                                            self.foundation_taxonomy)
+        result = str(result)
+        trimmed_tree = '(CBB3:0.44621,PBB1:0.08710999999999999)0.801:0.14776;\n'
+        self.assertEqual(result, trimmed_tree)
+
+    def test_graft_functions(self):
+        result = _graft_functions(self.graft_letter_g)
+        self.assertEqual(result, (6, 'g'))
 
     def test_create_taxonomy_dic_many_genus(self):
 
@@ -69,7 +78,6 @@ def test_create_taxonomy_dic_many_genus(self):
 
         result = _create_taxonomy_dict(self.extension_taxonomy,
                                        self.graft_level_6)
-        print('\n\n\nlalala', result)
         self.assertDictEqual(result, test)
 
     def test_create_taxonomy_dic_none(self):