small fix to cover

phykit/services/tree/covarying_evolutionary_rates.py

@@ -43,8 +43,7 @@ def run(self):
 
         # obtain corrected branch lengths where branch lengths
         # are corrected by the species tree branch length
-        tree_zero_corr_branch_lengths = self.correct_branch_lengths(tree_zero, tree_ref)
-        tree_one_corr_branch_lengths = self.correct_branch_lengths(tree_one, tree_ref)
+        tree_zero_corr_branch_lengths, tree_one_corr_branch_lengths = self.correct_branch_lengths(tree_zero, tree_one, tree_ref)
 
         # remove corrected BLs greater than 5
         outlier_indices = []
@@ -102,32 +101,7 @@ def remove_outliers_based_on_indices(self, corr_branch_lengths, outlier_indices)
         """
         corr_branch_lengths = [i for j, i in enumerate(corr_branch_lengths) if j not in outlier_indices]
         return corr_branch_lengths
-
-    # def shared_tips(
-    #     self, 
-    #     a,
-    #     b
-    #     ):
-    #     """
-    #     Determines what tips are shared between two trees
-    #     -------------------------------------------------
-    #     argv: a
-    #         list of tips from one tree
-    #     argv: b
-    #         list of tips from a second tree
-    #     """ 
-
-    #     a_set = set(a) 
-    #     b_set = set(b) 
-
-    #     # check length  
-    #     if len(a_set.intersection(b_set)) > 0: 
-    #         return(list(a_set.intersection(b_set)))   
-    #     else: 
-    #         print("no common tips") 
-    #         sys.exit()
 
-
     def prune_tips(
         self, tree, tips
         ):
@@ -195,39 +169,49 @@ def determine_if_clade_differs(
 
     def correct_branch_lengths(
         self, 
-        t,
+        t0,
+        t1,
         sp
         ):
         """
         obtain a list of corrected branch lengths
         """
 
-        l = []
-        for i, s in zip(t.get_terminals(), sp.get_terminals()):
-            newtree = copy.deepcopy(sp)
-
-            # get tree tip names
-            tree_zero_tips = self.get_tip_names_from_tree(i)
+        l0 = []
+        l1 = []
+        for i, s in zip(t0.get_terminals(), sp.get_terminals()):
+            for term in sp.get_terminals():
+                if set(term.name)==set(i.name):
+                    l0.append(i.branch_length/s.branch_length)
 
-            for term in newtree.get_terminals():
+            for term in t1.get_terminals():
                 if set(term.name)==set(i.name):
-                    l.append(i.branch_length/s.branch_length)
+                    l1.append(i.branch_length/s.branch_length)
 
-        for i, s in zip(t.get_nonterminals(), sp.get_nonterminals()):
+        for i, s in zip(t0.get_nonterminals(), sp.get_nonterminals()):
             newtree = copy.deepcopy(sp)
+            newtree1 = copy.deepcopy(t1)
 
             # get tree tip names
             tree_zero_tips = self.get_tip_names_from_tree(i)
 
             newtree = newtree.common_ancestor(tree_zero_tips)
-
+            newtree1 = newtree1.common_ancestor(tree_zero_tips)
+
             for nonterm in newtree.get_nonterminals():
                 try:
-                    l.append(i.branch_length/nonterm.branch_length)
+                    l0.append(i.branch_length/nonterm.branch_length)
+                except: 
+                    l0.append("NA")
+                break
+
+            for nonterm in newtree1.get_nonterminals():
+                try:
+                    l1.append(i.branch_length/nonterm.branch_length)
                 except: 
-                    l.append("NA")
+                    l1.append("NA")
                 break
 
 
 
-        return(l)
+        return(l0, l1)

phykit/version.py

@@ -1 +1 @@
-__version__ = '1.11.9'
+__version__ = '1.11.10'

tests/integration/tree/test_covarying_evolutionary_rates_integration.py

@@ -14,7 +14,7 @@
 class TestCovaryingEvolutionaryRates(object):
     @patch("builtins.print")
     def test_covarying_evolutionary_rates(self, mocked_print):
-        expected_result = "0.5436\t0.054828"
+        expected_result = "0.5755\t0.03959"
         testargs = [
             "phykit",
             "covarying_evolutionary_rates",
@@ -29,7 +29,7 @@ def test_covarying_evolutionary_rates(self, mocked_print):
 
     @patch("builtins.print")
     def test_covarying_evolutionary_rates_alias(self, mocked_print):
-        expected_result = "0.5436\t0.054828"
+        expected_result = "0.5755\t0.03959"
         testargs = [
             "phykit",
             "cover",
@@ -56,19 +56,19 @@ def test_covarying_evolutionary_rates_verbose(self, mocked_print):
         with patch.object(sys, "argv", testargs):
             Phykit()
         assert mocked_print.mock_calls == [
-            call(f"{-0.333}\t{-1.3686}"),
-            call(f"{0.2747}\t{1.7774}"),
-            call(f"{0.2747}\t{0.0691}"),
-            call(f"{1.3905}\t{0.5971}"),
-            call(f"{0.2747}\t{-0.2188}"),
-            call(f"{0.2747}\t{0.0691}"),
-            call(f"{-0.3428}\t{-0.223}"),
-            call(f"{-3.1873}\t{-1.5688}"),
-            call(f"{0.2747}\t{0.0691}"),
-            call(f"{0.2747}\t{1.5686}"),
-            call(f"{0.2747}\t{-1.4737}"),
-            call(f"{0.2747}\t{0.0691}"),
-            call(f"{0.2747}\t{0.6333}")
+            call(f"{-0.333}\t{-0.2246}"),
+            call(f"{0.2747}\t{0.1191}"),
+            call(f"{0.2747}\t{0.1191}"),
+            call(f"{1.3905}\t{0.7501}"),
+            call(f"{0.2747}\t{0.1191}"),
+            call(f"{0.2747}\t{0.1191}"),
+            call(f"{-0.3428}\t{-0.2302}"),
+            call(f"{-3.1873}\t{-1.8388}"),
+            call(f"{0.2747}\t{0.1191}"),
+            call(f"{0.2747}\t{-1.3055}"),
+            call(f"{0.2747}\t{2.6302}"),
+            call(f"{0.2747}\t{0.1191}"),
+            call(f"{0.2747}\t{-0.4956}")
         ]
 
     @patch("builtins.print")
@@ -169,7 +169,7 @@ def test_covarying_evolutionary_rates_tree_topologies_do_not_match(self, mocked_
 
     @patch("builtins.print")
     def test_covarying_evolutionary_rates(self, mocked_print):
-        expected_result = "0.5874\t0.044626"
+        expected_result = "0.5755\t0.03959"
         testargs = [
             "phykit",
             "covarying_evolutionary_rates",