phylogenie 3.1.6__py3-none-any.whl → 3.1.8__py3-none-any.whl

phylogenie/__init__.py

@@ -1,4 +1,11 @@
-from phylogenie.draw import Coloring, draw_tree
+from phylogenie.draw import (
+    draw_colored_dated_tree_categorical,
+    draw_colored_dated_tree_continuous,
+    draw_colored_tree_categorical,
+    draw_colored_tree_continuous,
+    draw_dated_tree,
+    draw_tree,
+)
 from phylogenie.generators import (
     AliSimDatasetGenerator,
     BDEITreeDatasetGenerator,
@@ -11,8 +18,8 @@ from phylogenie.generators import (
     FBDTreeDatasetGenerator,
     TreeDatasetGeneratorConfig,
 )
-from phylogenie.io import load_fasta
-from phylogenie.msa import MSA
+from phylogenie.io import dump_fasta, load_fasta
+from phylogenie.msa import MSA, Sequence
 from phylogenie.skyline import (
     SkylineMatrix,
     SkylineMatrixCoercible,
@@ -64,7 +71,11 @@ from phylogenie.treesimulator import (
 )
 
 __all__ = [
-    "Coloring",
+    "draw_colored_dated_tree_categorical",
+    "draw_colored_dated_tree_continuous",
+    "draw_colored_tree_categorical",
+    "draw_colored_tree_continuous",
+    "draw_dated_tree",
     "draw_tree",
     "AliSimDatasetGenerator",
     "BDEITreeDatasetGenerator",
@@ -76,8 +87,10 @@ __all__ = [
     "EpidemiologicalTreeDatasetGenerator",
     "FBDTreeDatasetGenerator",
     "TreeDatasetGeneratorConfig",
+    "dump_fasta",
     "load_fasta",
     "MSA",
+    "Sequence",
     "SkylineMatrix",
     "SkylineMatrixCoercible",
     "SkylineParameter",

phylogenie/draw.py

@@ -10,7 +10,12 @@ from matplotlib.axes import Axes
 from matplotlib.colors import Colormap
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes  # pyright: ignore
 
-from phylogenie.treesimulator import Tree, get_node_depth_levels, get_node_depths
+from phylogenie.treesimulator import (
+    Tree,
+    get_node_ages,
+    get_node_depth_levels,
+    get_node_depths,
+)
 
 
 @dataclass
@@ -54,13 +59,12 @@ def draw_tree(
         colors = {node: colors for node in tree}
 
     xs = (
-        get_node_depth_levels(tree)
+        get_node_ages(tree)
+        if backward_time
+        else get_node_depth_levels(tree)
         if any(node.branch_length is None for node in tree.iter_descendants())
         else get_node_depths(tree)
     )
-    if backward_time:
-        max_x = max(xs.values())
-        xs = {node: max_x - x for node, x in xs.items()}
 
     ys: dict[Tree, float] = {node: i for i, node in enumerate(tree.get_leaves())}
     for node in tree.postorder_traversal():

phylogenie/io/__init__.py

@@ -1,3 +1,3 @@
-from phylogenie.io.fasta import load_fasta
+from phylogenie.io.fasta import dump_fasta, load_fasta
 
-__all__ = ["load_fasta"]
+__all__ = ["load_fasta", "dump_fasta"]

phylogenie/treesimulator/__init__.py

@@ -27,11 +27,14 @@ from phylogenie.treesimulator.utils import (
     compute_sackin_index,
     get_distance,
     get_mrca,
+    get_node_ages,
     get_node_depth_levels,
     get_node_depths,
     get_node_height_levels,
     get_node_heights,
     get_node_leaf_counts,
+    get_node_times,
+    get_path,
 )
 
 __all__ = [
@@ -65,9 +68,12 @@ __all__ = [
     "compute_sackin_index",
     "get_distance",
     "get_mrca",
+    "get_node_ages",
     "get_node_depth_levels",
     "get_node_depths",
     "get_node_height_levels",
     "get_node_heights",
     "get_node_leaf_counts",
+    "get_node_times",
+    "get_path",
 ]

phylogenie/treesimulator/features.py

@@ -5,11 +5,13 @@ from phylogenie.treesimulator.events.mutations import get_mutation_id
 from phylogenie.treesimulator.model import get_node_state
 from phylogenie.treesimulator.tree import Tree
 from phylogenie.treesimulator.utils import (
+    get_node_ages,
     get_node_depth_levels,
     get_node_depths,
     get_node_height_levels,
     get_node_heights,
     get_node_leaf_counts,
+    get_node_times,
 )
 
 
@@ -22,6 +24,7 @@ def _get_mutations(tree: Tree) -> dict[Tree, int]:
 
 
 class Feature(str, Enum):
+    AGE = "age"
     DEPTH = "depth"
     DEPTH_LEVEL = "depth_level"
     HEIGHT = "height"
@@ -29,9 +32,11 @@ class Feature(str, Enum):
     MUTATION = "mutation"
     N_LEAVES = "n_leaves"
     STATE = "state"
+    TIME = "time"
 
 
 FEATURES_EXTRACTORS = {
+    Feature.AGE: get_node_ages,
     Feature.DEPTH: get_node_depths,
     Feature.DEPTH_LEVEL: get_node_depth_levels,
     Feature.HEIGHT: get_node_heights,
@@ -39,6 +44,7 @@ FEATURES_EXTRACTORS = {
     Feature.MUTATION: _get_mutations,
     Feature.N_LEAVES: get_node_leaf_counts,
     Feature.STATE: _get_states,
+    Feature.TIME: get_node_times,
 }
 
 

phylogenie/treesimulator/tree.py

@@ -153,6 +153,16 @@ class Tree(MetadataMixin):
             child.branch_length_or_raise() + child.height for child in self.children
         )
 
+    @property
+    def time(self) -> float:
+        return self.depth
+
+    @property
+    def age(self) -> float:
+        if self.parent is None:
+            return self.height
+        return self.parent.age - self.branch_length_or_raise()
+
     # -------------
     # Miscellaneous
     # -------------

phylogenie/treesimulator/utils.py

@@ -51,6 +51,17 @@ def get_node_heights(tree: Tree) -> dict[Tree, float]:
     return heights
 
 
+def get_node_times(tree: Tree) -> dict[Tree, float]:
+    return get_node_depths(tree)
+
+
+def get_node_ages(tree: Tree) -> dict[Tree, float]:
+    ages: dict[Tree, float] = {tree: tree.height}
+    for node in tree.iter_descendants():
+        ages[node] = ages[node.parent] - node.branch_length  # pyright: ignore
+    return ages
+
+
 def get_mrca(node1: Tree, node2: Tree) -> Tree:
     node1_ancestors = set(node1.iter_upward())
     for node2_ancestor in node2.iter_upward():

{phylogenie-3.1.6.dist-info → phylogenie-3.1.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylogenie
-Version: 3.1.6
+Version: 3.1.8
 Summary: Generate phylogenetic datasets with minimal setup effort
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown

{phylogenie-3.1.6.dist-info → phylogenie-3.1.8.dist-info}/RECORD

@@ -1,5 +1,5 @@
-phylogenie/__init__.py,sha256=-4GKO2EKgc2GiOhzVRI0SQk6wQZ4AlP7Ron_Lp-s_r0,2913
-phylogenie/draw.py,sha256=djG0cG9mmNFZ7vf3jo8Ei3bNBJVqujp6gtZtwPxyfSY,23341
+phylogenie/__init__.py,sha256=redo-SdvWwQPlyqOfdSW0TkkZf-aP98kLRCUIg4pB8c,3304
+phylogenie/draw.py,sha256=J_ijON8O848f-r2VnOu8MbSR_vAcvO8zPq5u5Vq5J_U,23323
 phylogenie/main.py,sha256=ry3B3HiwibZG3_qB58T5UhWy5dp6neYUtSqzL9LrSkA,1698
 phylogenie/mixins.py,sha256=wMwqP6zkqME9eMyzx5FS6-p9X8yW09jIC8jge8pHlkk,907
 phylogenie/msa.py,sha256=JDGyZUsAq6-m-SQjoCDjAkAZIxfgyl_PDIhdYn5HOow,2064
@@ -13,18 +13,18 @@ phylogenie/generators/dataset.py,sha256=Z3a4Mhh6zMTYmhd-aIT3aCaJMTVg4I_QvWWIrCw2
 phylogenie/generators/factories.py,sha256=2mTFdFbbLyV3v79JaOEVtqLOmxQHaOUv1S-Y3vVo7U0,8480
 phylogenie/generators/trees.py,sha256=8dO1CkU34E6mmMAHrYqiLV_VA8r54cSEOo-UzoHiN20,10467
 phylogenie/generators/typeguards.py,sha256=yj4VkhOaUXJ2OrY-6zhOeY9C4yKIQxjZtk2d-vIxttQ,828
-phylogenie/io/__init__.py,sha256=eWDU6YDqAdx6TZlUMmMbsfO8gP3i5HP_cfUe_-0x2FA,69
+phylogenie/io/__init__.py,sha256=3v_bxv9RVeQ3KZzxNFeV9KLVxaC_Whf7rgWLnBKoEr0,95
 phylogenie/io/fasta.py,sha256=kx9uVATLpzpXdhhNNMvMpB5Vdwh9CTWepTGachvEwV4,1154
 phylogenie/skyline/__init__.py,sha256=7pF4CUb4ZCLzNYJNhOjpuTOLTRhlK7L6ugfccNqjIGo,620
 phylogenie/skyline/matrix.py,sha256=v4SitY7VbXprqlqQckjWTzW5hwRmCyIF595R6IJMxWw,9268
 phylogenie/skyline/parameter.py,sha256=TVqkqirGXNN-VP8hnIJACPkOxUan6LkGa5o_JcPfwbY,4834
 phylogenie/skyline/vector.py,sha256=60jtp7PieiEaEH0Tp6zNjNKjyzpN_nT5uwBUXbgeATk,7261
-phylogenie/treesimulator/__init__.py,sha256=Qz__cFookXuEjq8AUp1A6XRON0qQ_xX-q2Q5ixP4XUg,1791
-phylogenie/treesimulator/features.py,sha256=XbuwGw8xjGs2lNhJvvUUvXVtheSTBaSN6qj39tWYEro,1391
+phylogenie/treesimulator/__init__.py,sha256=D4VX2JLEcmuSVpANCRXyZvEfZ13LrFY5YElPxU1Wx-w,1903
+phylogenie/treesimulator/features.py,sha256=x1Gp1IpQeW-gJ6etdnXPgeJQ1_qsKoefIuqjzwAINDg,1530
 phylogenie/treesimulator/gillespie.py,sha256=ey2hdpJOSpNW88duwK7wTAdYSTnSuTSZ_yhZv9MlNHo,5323
 phylogenie/treesimulator/model.py,sha256=L0RsL6H1ynFDPecULniSs4Cs8dvz87ovviQOXFy5Qt0,4580
-phylogenie/treesimulator/tree.py,sha256=DEdzCh4vABq2f095beh3tD3_aee7EyXPDSjcyHKgKLg,6064
-phylogenie/treesimulator/utils.py,sha256=OxZwVHxN004Jf-kYZ_GfJgIY0beo-0tYq80CuFGQt-M,3416
+phylogenie/treesimulator/tree.py,sha256=1slBjrlggWiQiQgVg45Xuklhmq-n4H5obEAhPvWEi8c,6303
+phylogenie/treesimulator/utils.py,sha256=-8_HG2FICsJ2eBPomtQSZUaHH1QE-r2s0UsGC3Zb5Yk,3744
 phylogenie/treesimulator/events/__init__.py,sha256=w2tJ0D2WB5AiCbr3CsKN6vdADueiAEMzd_ve0rpa4zg,939
 phylogenie/treesimulator/events/base.py,sha256=JQKYUZmhB2Q-WQOy2ULGKQiabsMz-JvwMVfDoa3ZKyo,1170
 phylogenie/treesimulator/events/contact_tracing.py,sha256=t64omKEO2d-DfN_dhDJlXp_Kg9egy2ZE346yWjV3ZrA,5148
@@ -33,9 +33,9 @@ phylogenie/treesimulator/events/mutations.py,sha256=8Nqa2fg7fwaVNe5XSkGDSwp9pIKQ
 phylogenie/treesimulator/io/__init__.py,sha256=rfP-zp8SP8baq5_4dPAr10WH0W6KfoMCxdTZDCSXtzE,185
 phylogenie/treesimulator/io/newick.py,sha256=8Pr_jixByPOaVch18w-rFt62HYy0U97YMu0H-QSwIy0,3449
 phylogenie/treesimulator/io/nexus.py,sha256=zqT9dzj413z_s0hqp3Cdq5NMO6lv-zuuaJlaqzaqaB8,1847
-phylogenie-3.1.6.dist-info/licenses/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-3.1.6.dist-info/METADATA,sha256=az3fV29mfXpVsyxK5PDssutWcvaLnu_MLfHO4pgyBas,5194
-phylogenie-3.1.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-phylogenie-3.1.6.dist-info/entry_points.txt,sha256=BBH8LoReHnNFnvq4sROEsVFegfkKJ6c_oHZ7bgK7Jl4,52
-phylogenie-3.1.6.dist-info/top_level.txt,sha256=1YGZJhKA9tN9qI0Hcj6Cn_sOoDpba0HQlNcgQTjMD-8,11
-phylogenie-3.1.6.dist-info/RECORD,,
+phylogenie-3.1.8.dist-info/licenses/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-3.1.8.dist-info/METADATA,sha256=0lQMRPORgVWh0cp4OYt1RjCkYtCdy2P3ugiBmqB2oHQ,5194
+phylogenie-3.1.8.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+phylogenie-3.1.8.dist-info/entry_points.txt,sha256=BBH8LoReHnNFnvq4sROEsVFegfkKJ6c_oHZ7bgK7Jl4,52
+phylogenie-3.1.8.dist-info/top_level.txt,sha256=1YGZJhKA9tN9qI0Hcj6Cn_sOoDpba0HQlNcgQTjMD-8,11
+phylogenie-3.1.8.dist-info/RECORD,,