phykit 2.1.46__tar.gz → 2.1.48__tar.gz

{phykit-2.1.46 → phykit-2.1.48}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phykit
-Version: 2.1.46
+Version: 2.1.48
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

{phykit-2.1.46 → phykit-2.1.48}/phykit/cli_registry.py

@@ -88,6 +88,8 @@ ALIAS_TO_HANDLER: Dict[str, str] = {
     "pgls": "phylogenetic_regression",
     "phylo_glm": "phylogenetic_glm",
     "pglm": "phylogenetic_glm",
+    "parsimony": "parsimony_score",
+    "pars": "parsimony_score",
     "pic": "independent_contrasts",
     "phylo_contrasts": "independent_contrasts",
     "asr": "ancestral_state_reconstruction",

{phykit-2.1.46 → 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-2.1.46 → phykit-2.1.48}/phykit/phykit.py

@@ -163,6 +163,8 @@ class Phykit:
                 ===================
                 independent_contrasts (alias: pic; phylo_contrasts)
                     - Felsenstein's phylogenetically independent contrasts
+                parsimony_score (alias: parsimony; pars)
+                    - Fitch parsimony score of a tree given an alignment
                 ancestral_state_reconstruction (alias: asr; anc_recon)
                     - estimate ancestral states for continuous traits using
                       ML (fast or VCV-based) with optional contMap plot
@@ -1679,6 +1681,62 @@ class Phykit:
         _run_service(parser, argv, VariableSites)
 
     ## Tree functions
+    @staticmethod
+    def parsimony_score(argv):
+        parser = _new_parser(
+            description=textwrap.dedent(
+                f"""\
+                {help_header}
+
+                Compute the Fitch (1971) maximum parsimony score of a
+                tree given an alignment.
+
+                The parsimony score is the minimum number of character
+                state changes required to explain the alignment on the
+                given tree topology. Each site is scored independently
+                using the Fitch downpass algorithm.
+
+                Gap characters (-, N, X, ?) are treated as wildcards.
+                Multifurcations are automatically resolved.
+
+                Cross-validated against R's phangorn::parsimony().
+
+                Aliases:
+                  parsimony_score, parsimony, pars
+                Command line interfaces:
+                  pk_parsimony_score, pk_parsimony, pk_pars
+
+                Usage:
+                phykit parsimony_score -t <tree> -a <alignment>
+                  [-v/--verbose] [--json]
+
+                Options
+                =====================================================
+                -t/--tree                   tree file (required)
+
+                -a/--alignment              alignment file in FASTA
+                                            format (required)
+
+                -v/--verbose                print per-site parsimony
+                                            scores
+
+                --json                      optional argument to output
+                                            results as JSON
+                """
+            ),
+        )
+        parser.add_argument(
+            "-t", "--tree", type=str, required=True, help=SUPPRESS, metavar=""
+        )
+        parser.add_argument(
+            "-a", "--alignment", type=str, required=True, help=SUPPRESS, metavar=""
+        )
+        parser.add_argument(
+            "-v", "--verbose", action="store_true", required=False, help=SUPPRESS
+        )
+        _add_json_argument(parser)
+        _run_service(parser, argv, ParsimonyScore)
+
     @staticmethod
     def independent_contrasts(argv):
         parser = _new_parser(
@@ -4689,7 +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).
@@ -4715,7 +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;
@@ -6725,6 +6785,10 @@ def variable_sites(argv=None):
 
 
 # Tree-based functions
+def parsimony_score(argv=None):
+    Phykit.parsimony_score(sys.argv[1:])
+
+
 def independent_contrasts(argv=None):
     Phykit.independent_contrasts(sys.argv[1:])
 

{phykit-2.1.46 → phykit-2.1.48}/phykit/service_factories.py

@@ -83,6 +83,7 @@ RelativeRateTest = _LazyServiceFactory("phykit.services.tree.relative_rate_test"
 ThresholdModel = _LazyServiceFactory("phykit.services.tree.threshold_model", "ThresholdModel")
 PolytomyTest = _LazyServiceFactory("phykit.services.tree.polytomy_test", "PolytomyTest")
 PrintTree = _LazyServiceFactory("phykit.services.tree.print_tree", "PrintTree")
+ParsimonyScore = _LazyServiceFactory("phykit.services.tree.parsimony_score", "ParsimonyScore")
 PhyloHeatmap = _LazyServiceFactory("phykit.services.tree.phylo_heatmap", "PhyloHeatmap")
 PruneTree = _LazyServiceFactory("phykit.services.tree.prune_tree", "PruneTree")
 QuartetPie = _LazyServiceFactory("phykit.services.tree.quartet_pie", "QuartetPie")

{phykit-2.1.46 → phykit-2.1.48}/phykit/services/tree/__init__.py

@@ -27,6 +27,7 @@ _EXPORTS = {
     "RelativeRateTest": "relative_rate_test",
     "PolytomyTest": "polytomy_test",
     "PrintTree": "print_tree",
+    "ParsimonyScore": "parsimony_score",
     "PhyloHeatmap": "phylo_heatmap",
     "PruneTree": "prune_tree",
     "QuartetPie": "quartet_pie",

phykit-2.1.48/phykit/services/tree/parsimony_score.py

@@ -0,0 +1,169 @@
+"""
+Maximum parsimony score of a tree given an alignment.
+
+Computes the Fitch (1971) parsimony score — the minimum number of
+character state changes required to explain the alignment on the
+given tree topology. Each site is scored independently and the
+total is summed.
+
+Cross-validated against R's phangorn::parsimony().
+"""
+import copy
+from typing import Dict, List
+
+from Bio import SeqIO
+
+from .base import Tree
+from ...helpers.json_output import print_json
+from ...errors import PhykitUserError
+
+
+class ParsimonyScore(Tree):
+    def __init__(self, args) -> None:
+        parsed = self.process_args(args)
+        super().__init__(tree_file_path=parsed["tree_file_path"])
+        self.alignment_path = parsed["alignment_path"]
+        self.verbose = parsed["verbose"]
+        self.json_output = parsed["json_output"]
+
+    def run(self) -> None:
+        tree = self.read_tree_file()
+        tree = copy.deepcopy(tree)
+        self._validate_tree(tree)
+        self._resolve_polytomies(tree)
+
+        sequences = self._parse_alignment(self.alignment_path)
+
+        # Prune to shared taxa
+        tree_tips = set(t.name for t in tree.get_terminals())
+        seq_taxa = set(sequences.keys())
+        shared = tree_tips & seq_taxa
+        if len(shared) < 3:
+            raise PhykitUserError(
+                [
+                    f"Only {len(shared)} shared taxa between tree and alignment.",
+                    "At least 3 shared taxa are required.",
+                ],
+                code=2,
+            )
+
+        tips_to_prune = list(tree_tips - shared)
+        if tips_to_prune:
+            tree = self.prune_tree_using_taxa_list(tree, tips_to_prune)
+            self._resolve_polytomies(tree)
+
+        sequences = {t: sequences[t] for t in shared}
+        aln_length = len(next(iter(sequences.values())))
+
+        total_score, per_site = self._fitch_parsimony(tree, sequences, aln_length)
+
+        if self.json_output:
+            payload = {
+                "parsimony_score": total_score,
+                "alignment_length": aln_length,
+                "n_taxa": len(shared),
+            }
+            if self.verbose:
+                payload["per_site_scores"] = per_site
+            print_json(payload)
+        else:
+            print(total_score)
+            if self.verbose:
+                print()
+                for i, score in enumerate(per_site, 1):
+                    print(f"{i}\t{score}")
+
+    def process_args(self, args) -> Dict:
+        return dict(
+            tree_file_path=args.tree,
+            alignment_path=args.alignment,
+            verbose=getattr(args, "verbose", False),
+            json_output=getattr(args, "json", False),
+        )
+
+    def _validate_tree(self, tree) -> None:
+        tips = list(tree.get_terminals())
+        if len(tips) < 3:
+            raise PhykitUserError(
+                ["Tree must have at least 3 tips."], code=2
+            )
+
+    def _resolve_polytomies(self, tree) -> None:
+        from Bio.Phylo import Newick
+        for clade in tree.find_clades(order="postorder"):
+            while len(clade.clades) > 2:
+                child1 = clade.clades.pop()
+                child2 = clade.clades.pop()
+                new_internal = Newick.Clade(branch_length=0.0)
+                new_internal.clades = [child1, child2]
+                clade.clades.append(new_internal)
+
+    def _parse_alignment(self, path: str) -> Dict[str, str]:
+        try:
+            records = list(SeqIO.parse(path, "fasta"))
+        except Exception:
+            raise PhykitUserError(
+                [f"Could not parse alignment from {path}."], code=2
+            )
+        if not records:
+            raise PhykitUserError(
+                ["Alignment file is empty."], code=2
+            )
+        sequences = {r.id: str(r.seq).upper() for r in records}
+
+        # Validate same length
+        lengths = set(len(s) for s in sequences.values())
+        if len(lengths) > 1:
+            raise PhykitUserError(
+                ["Sequences have different lengths. Provide an aligned FASTA file."],
+                code=2,
+            )
+        return sequences
+
+    def _fitch_parsimony(
+        self, tree, sequences: Dict[str, str], aln_length: int
+    ) -> tuple:
+        """Compute Fitch parsimony score.
+
+        For each site, performs a postorder (downpass) traversal:
+        - Terminal nodes: state set = {observed character}
+        - Internal nodes: if children share states, intersection;
+          otherwise union (and add 1 to score)
+
+        Gap characters (-) and ambiguous characters (N, X, ?) are
+        treated as wildcards (matching any state).
+        """
+        wildcard_chars = {"-", "N", "X", "?", "n", "x"}
+        all_states = {"A", "C", "G", "T"}
+        per_site = []
+        total_score = 0
+
+        for site_idx in range(aln_length):
+            site_score = 0
+            node_states = {}
+
+            for clade in tree.find_clades(order="postorder"):
+                if clade.is_terminal():
+                    char = sequences[clade.name][site_idx]
+                    if char in wildcard_chars:
+                        node_states[id(clade)] = set(all_states)
+                    else:
+                        node_states[id(clade)] = {char}
+                else:
+                    if len(clade.clades) != 2:
+                        continue
+                    left, right = clade.clades
+                    left_states = node_states.get(id(left), set(all_states))
+                    right_states = node_states.get(id(right), set(all_states))
+
+                    intersection = left_states & right_states
+                    if intersection:
+                        node_states[id(clade)] = intersection
+                    else:
+                        node_states[id(clade)] = left_states | right_states
+                        site_score += 1
+
+            per_site.append(site_score)
+            total_score += site_score
+
+        return total_score, per_site

{phykit-2.1.46 → 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-2.1.46 → phykit-2.1.48}/phykit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phykit
-Version: 2.1.46
+Version: 2.1.48
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

{phykit-2.1.46 → phykit-2.1.48}/phykit.egg-info/SOURCES.txt

@@ -84,6 +84,7 @@ phykit/services/tree/nearest_neighbor_interchange.py
 phykit/services/tree/network_signal.py
 phykit/services/tree/ou_shift_detection.py
 phykit/services/tree/ouwie.py
+phykit/services/tree/parsimony_score.py
 phykit/services/tree/patristic_distances.py
 phykit/services/tree/phenogram.py
 phykit/services/tree/phylo_heatmap.py

{phykit-2.1.46 → phykit-2.1.48}/phykit.egg-info/entry_points.txt

@@ -125,7 +125,10 @@ pk_pairwise_id = phykit.phykit:pairwise_identity
 pk_pairwise_identity = phykit.phykit:pairwise_identity
 pk_pal2nal = phykit.phykit:thread_dna
 pk_paqc = phykit.phykit:plot_alignment_qc
+pk_pars = phykit.phykit:parsimony_score
+pk_parsimony = phykit.phykit:parsimony_score
 pk_parsimony_informative_sites = phykit.phykit:parsimony_informative_sites
+pk_parsimony_score = phykit.phykit:parsimony_score
 pk_patristic_distances = phykit.phykit:patristic_distances
 pk_pd = phykit.phykit:patristic_distances
 pk_pdr = phykit.phykit:phylogenetic_ordination

{phykit-2.1.46 → phykit-2.1.48}/setup.py

@@ -101,6 +101,9 @@ setup(
             "pk_variable_sites = phykit.phykit:variable_sites",
             "pk_vs = phykit.phykit:variable_sites",
             "pk_ancestral_state_reconstruction = phykit.phykit:ancestral_state_reconstruction", # Tree-based functions
+            "pk_parsimony_score = phykit.phykit:parsimony_score",
+            "pk_parsimony = phykit.phykit:parsimony_score",
+            "pk_pars = phykit.phykit:parsimony_score",
             "pk_independent_contrasts = phykit.phykit:independent_contrasts",
             "pk_pic = phykit.phykit:independent_contrasts",
             "pk_phylo_contrasts = phykit.phykit:independent_contrasts",

phykit-2.1.46/phykit/version.py

@@ -1 +0,0 @@
-__version__ = "2.1.46"