phykit 2.1.47__tar.gz → 2.1.48__tar.gz

{phykit-2.1.47 → phykit-2.1.48}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phykit
-Version: 2.1.47
+Version: 2.1.48
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

{phykit-2.1.47 → phykit-2.1.48}/phykit/helpers/quartet_utils.py

@@ -2,8 +2,8 @@
 Shared utilities for quartet concordance factor computation and ASTRAL parsing.
 
 Provides gene concordance factor (gCF/gDF1/gDF2) computation via the
-four-group bipartition decomposition, and parsing of ASTRAL -t 2
-q1/q2/q3 annotations from Newick node labels.
+four-group bipartition decomposition, and parsing of ASTRAL -t 2 or
+wASTRAL --support 3 q1/q2/q3 annotations from Newick node labels.
 """
 from typing import Dict, List, Optional, Tuple
 
@@ -93,10 +93,11 @@ def compute_gcf_per_node(
 def parse_astral_annotations(
     tree,
 ) -> Dict[int, Tuple[float, float, float]]:
-    """Parse q1/q2/q3 annotations from ASTRAL -t 2 Newick node labels.
+    """Parse q1/q2/q3 annotations from ASTRAL/wASTRAL Newick node labels.
 
-    ASTRAL annotates internal nodes with formats like:
+    Supports ASTRAL -t 2 and wASTRAL --support 3 output formats:
       '[q1=0.5;q2=0.3;q3=0.2;f1=50;...]'
+      '[CULength=2.6;f1=108;...;q1=0.96;q2=0.03;q3=0.01]'
       'q1=0.5;q2=0.3;q3=0.2'
 
     Returns dict mapping clade id -> (q1, q2, q3).

{phykit-2.1.47 → phykit-2.1.48}/phykit/phykit.py

@@ -4747,7 +4747,8 @@ class Phykit:
                 In native mode (-g provided), computes gene concordance
                 factors (gCF, gDF1, gDF2) from a species tree and gene
                 trees via bipartition matching. In ASTRAL mode (no -g),
-                parses q1/q2/q3 annotations from ASTRAL -t 2 output.
+                parses q1/q2/q3 annotations from ASTRAL -t 2 output or
+                wASTRAL --support 3 output.
 
                 Pie slices show: concordant (blue), discordant alt 1
                 (red), discordant alt 2 (gray).
@@ -4773,7 +4774,8 @@ class Phykit:
 
                 -g/--gene-trees             gene trees file, one Newick
                                             tree per line (optional;
-                                            if omitted, ASTRAL -t 2
+                                            if omitted, ASTRAL -t 2 or
+                                            wASTRAL --support 3
                                             annotations are parsed)
 
                 -o/--output                 output figure path (required;

{phykit-2.1.47 → phykit-2.1.48}/phykit/services/tree/quartet_pie.py

@@ -5,7 +5,7 @@ Draws a phylogram with pie charts at internal nodes showing the
 proportion of gene trees supporting the species tree topology (gCF)
 versus the two NNI alternative topologies (gDF1, gDF2). Supports
 both native computation from gene trees and parsing of ASTRAL -t 2
-annotations.
+or wASTRAL --support 3 annotations.
 """
 import sys
 from typing import Dict, List, Tuple
@@ -50,7 +50,8 @@ class QuartetPie(Tree):
                     [
                         "No ASTRAL q1/q2/q3 annotations found in the tree.",
                         "Either provide gene trees with -g, or use an ASTRAL",
-                        "-t 2 output tree with quartet annotations.",
+                        "-t 2 or wASTRAL --support 3 output tree with quartet",
+                        "annotations.",
                     ],
                     code=2,
                 )

phykit-2.1.48/phykit/version.py

@@ -0,0 +1 @@
+__version__ = "2.1.48"

{phykit-2.1.47 → phykit-2.1.48}/phykit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phykit
-Version: 2.1.47
+Version: 2.1.48
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

phykit-2.1.47/phykit/version.py

@@ -1 +0,0 @@
-__version__ = "2.1.47"