added terminal branch names to verbose option of bss function

Author: JLSteenwyk

docs/usage/index.rst

@@ -30,8 +30,8 @@ Calling functions
    phykit <command> [optional command arguments]
 
 Command specific help messages can be viewed by adding a 
--h/\\-\\-help argument after the command. For example, to see the
-to see the help message for the command 'treeness', execute:
+-h/\\-\\-help argument after the command. For example, to see the help message
+for the command 'treeness', execute:
 
 .. code-block:: shell
 
@@ -650,6 +650,9 @@ High bipartition support values are thought to be desirable because
 they are indicative of greater certainty in tree topology.
 
 To obtain all bipartition support values, use the -v/\\-\\-verbose option.
+In addition to support values for each node, the names of all terminal
+branches tips are also included. Each terminal branch name is separated
+with a semi-colon (;).
 
 .. code-block:: shell
 
@@ -878,7 +881,7 @@ or otherwise.
 
 .. code-block:: shell
 
-   phykit internode_labeler <file> [-o/--output <file>]
+   phykit internode_labeler <tree> [-o/--output <file>]
 
 Options: |br|
 *<tree>*: first argument after function name should be a tree file |br|
@@ -1371,8 +1374,8 @@ Saturation is defined as sequences in multiple sequence
 alignments that have undergone numerous substitutions such
 that the distances between taxa are underestimated.
 
-Data with no saturation will have a value of 1. Completely
-saturated data will have a value of 0.  
+Data with no saturation will have a value of 1. The closer
+the value is to 1, the less saturated the data.
 
 Saturation is calculated following Philippe et al., PLoS 
 Biology (2011), doi: 10.1371/journal.pbio.1000602.

phykit/phykit.py

@@ -1146,6 +1146,9 @@ def bipartition_support_stats(argv):
                 they are indicative of greater certainty in tree topology.
 
                 To obtain all bipartition support values, use the -v/--verbose option.
+                In addition to support values for each node, the names of all terminal
+                branches tips are also included. Each terminal branch name is separated
+                with a semi-colon (;).
 
                 Aliases:
                   bipartition_support_stats, bss
@@ -1553,7 +1556,7 @@ def internode_labeler(argv):
                   pk_internode_labeler, pk_il
 
                 Usage:
-                phykit internode_labeler <file> [-o/--output <file>]
+                phykit internode_labeler <tree> [-o/--output <file>]
 
                 Options
                 =====================================================
@@ -2442,10 +2445,10 @@ def saturation(argv):
                 alignments that have undergone numerous substitutions such
                 that the distances between taxa are underestimated.
 
-                Data with no saturation will have a value of 1. Completely
-                saturated data will have a value of 0.  
+                Data with no saturation will have a value of 1. The closer
+                the value is to 1, the less saturated the data.
 
-                Saturation is calculated following Philippe et al., PLoS 
+                Saturation is calculated following Philippe et al., PLoS
                 Biology (2011), doi: 10.1371/journal.pbio.1000602.
 
                 Aliases: 

phykit/services/tree/bipartition_support_stats.py

@@ -11,12 +11,12 @@ def __init__(self, args) -> None:
 
     def run(self):
         tree = self.read_tree_file()
-        bs_vals = self.get_bipartition_support_vals(tree)
+        bs_vals, term_names = self.get_bipartition_support_vals(tree)
 
         if self.verbose:
             try:
-                for bs_val in bs_vals:
-                    print(bs_val)
+                for bs_val, names in zip(bs_vals, term_names):
+                    print(bs_val, ";".join(names))
             except BrokenPipeError:
                 pass
         else:
@@ -29,10 +29,15 @@ def process_args(self, args):
     def get_bipartition_support_vals(self, tree):
         # initialize list to hold bootstrap values
         bs_vals = []
+        term_names = []
 
         # populate bs_vals with bootstrap values
-        for terminal in tree.get_nonterminals():
+        for nonterminal in tree.get_nonterminals():
             # only include if a bootstrap value is present
-            if terminal.confidence != None:
-                bs_vals.append(terminal.confidence)
-        return bs_vals
+            if nonterminal.confidence != None:
+                bs_vals.append(nonterminal.confidence)
+                temp = []
+                for term in nonterminal.get_terminals():
+                    temp.append(term.name)
+                term_names.append(temp)
+        return bs_vals, term_names

phykit/version.py

@@ -1 +1 @@
-__version__ = "1.19.6"
+__version__ = "1.19.7"

tests/integration/tree/test_bipartition_support_stats_integration.py

@@ -45,13 +45,13 @@ def test_bipartition_support_stats_verbose(self, mocked_print):
             Phykit()
 
         assert mocked_print.mock_calls == [
-            call(85),
-            call(85),
-            call(100),
-            call(100),
-            call(100),
-            call(100),
-            call(100),
+            call(85, "Aspergillus_fischeri_IBT_3007;Aspergillus_fischeri_NRRL181.GCF_000149645.1_ASM14964v1;Aspergillus_fischeri_NRRL4585;Aspergillus_fumigatus_Af293;Aspergillus_fumigatus_CEA10;Aspergillus_fumigatus_HMR_AF_270;Aspergillus_fumigatus_Z5;Aspergillus_oerlinghausenensis_CBS139183"),
+            call(85, "Aspergillus_fischeri_NRRL181.GCF_000149645.1_ASM14964v1;Aspergillus_fischeri_NRRL4585;Aspergillus_fumigatus_Af293;Aspergillus_fumigatus_CEA10;Aspergillus_fumigatus_HMR_AF_270;Aspergillus_fumigatus_Z5;Aspergillus_oerlinghausenensis_CBS139183"),
+            call(100, "Aspergillus_fischeri_NRRL4585;Aspergillus_fumigatus_Af293;Aspergillus_fumigatus_CEA10;Aspergillus_fumigatus_HMR_AF_270;Aspergillus_fumigatus_Z5;Aspergillus_oerlinghausenensis_CBS139183"),
+            call(100, "Aspergillus_fumigatus_Af293;Aspergillus_fumigatus_CEA10;Aspergillus_fumigatus_HMR_AF_270;Aspergillus_fumigatus_Z5;Aspergillus_oerlinghausenensis_CBS139183"),
+            call(100, "Aspergillus_fumigatus_Af293;Aspergillus_fumigatus_CEA10;Aspergillus_fumigatus_HMR_AF_270;Aspergillus_fumigatus_Z5"),
+            call(100, "Aspergillus_fumigatus_Af293;Aspergillus_fumigatus_CEA10"),
+            call(100, "Aspergillus_fumigatus_HMR_AF_270;Aspergillus_fumigatus_Z5"),
         ]
 
     @patch("builtins.print")
@@ -87,4 +87,4 @@ def test_bipartition_support_stats_alias(self, mocked_print):
             call("maximum: 100"),
             call("standard deviation: 7.3193"),
             call("variance: 53.5714")
-        ]
+        ]