cleaned up evolutionary rate analysis

phykit/services/tree/dvmc.py

@@ -1,71 +1,5 @@
-# import math
-# from typing import Tuple
-
-# from .base import Tree
-
-
-# class DVMC(Tree):
-#     def __init__(self, args) -> None:
-#         super().__init__(**self.process_args(args))
-
-#     def run(self):
-#         tree = self.read_tree_file()
-#         dvmc = self.determine_dvmc(tree)
-
-#         print(round(dvmc, 4))
-
-#     def process_args(self, args):
-#         return dict(tree_file_path=args.tree)
-
-#     def get_term_to_root_dist_and_sum_of_distances(self, tree) -> Tuple[float, float]:
-#         """
-#         calculate root to tip distances and
-#         the sum of root to tip distances
-#         """
-#         dist = []
-#         sum_dist = 0
-#         for term in tree.get_terminals():
-#             # append root to tip distance to dist
-#             dist.append((tree.distance(term)))
-#             # keep running sum of tree distances
-#             sum_dist += tree.distance(term)
-
-#         return dist, sum_dist
-
-#     def calculate_dvmc(self, dist: float, sum_dist: float, num_spp: int) -> float:
-#         """
-#         calculate dvmc from tip to root distances
-#         """
-#         # determine dvmc
-#         # calculate average tree distance
-#         avg_dist = sum_dist / num_spp
-
-#         # determine the sum of i=1 to N for (x_i-x_bar)^2
-#         sumi2N = float(0.0)
-#         for x_i in dist:
-#             sumi2N += (x_i - avg_dist) ** 2
-
-#         # multiply sumi2N by 1/(N-1) where N is the number of spp
-#         # and then take the square root
-#         dvmc = float(0.0)
-#         dvmc = math.sqrt((1 / (num_spp - 1)) * sumi2N)
-
-#         return dvmc
-
-#     def determine_dvmc(self, tree: Tree):
-#         # loop through terminal branches and store
-#         # distances from the root to the tip in a list.
-#         # Also, calc the sum of all tip to root distances
-#         dist, sum_dist = self.get_term_to_root_dist_and_sum_of_distances(tree)
-
-#         # determine number of taxa in the tree
-#         num_spp = tree.count_terminals()
-
-#         # calculate and return dvmc
-#         return self.calculate_dvmc(dist, sum_dist, num_spp)
-
-
 import math
+from typing import Dict
 
 from Bio.Phylo import Newick
 
@@ -81,7 +15,7 @@ def run(self):
         dvmc = self.determine_dvmc(tree)
         print(round(dvmc, 4))
 
-    def process_args(self, args):
+    def process_args(self, args) -> Dict[str, str]:
         return dict(tree_file_path=args.tree)
 
     def determine_dvmc(self, tree: Newick.Tree) -> float:

phykit/services/tree/evolutionary_rate.py

@@ -1,22 +1,17 @@
+from typing import Dict
+
 from .base import Tree
 
 
 class EvolutionaryRate(Tree):
     def __init__(self, args) -> None:
         super().__init__(**self.process_args(args))
 
-    def run(self):
+    def run(self) -> None:
         tree = self.read_tree_file()
-        total_tree_length = self.calculate_total_tree_length(tree)
+        total_tree_length = tree.total_branch_length()
         num_terminals = tree.count_terminals()
         print(round(total_tree_length / num_terminals, 4))
 
-    def process_args(self, args):
+    def process_args(self, args) -> Dict[str, str]:
         return dict(tree_file_path=args.tree)
-
-    def calculate_total_tree_length(self, tree):
-        total_len = float(0.0)
-        total_len = tree.total_branch_length()
-
-        if isinstance(total_len, (int, float)):
-            return total_len

tests/integration/tree/test_evolutionary_rate.py

@@ -1,9 +1,7 @@
 import pytest
 import sys
-from math import isclose
 from mock import patch, call
 from pathlib import Path
-from textwrap import dedent
 
 from phykit.phykit import Phykit