msasim 25.10.15__cp36-cp36m-win_amd64.whl → 25.11.2__cp36-cp36m-win_amd64.whl

_Sailfish/__init__.pyi

@@ -376,6 +376,8 @@ class modelFactory:
         ...
     def set_invariant_sites_proportion(self, arg0: float) -> None:
         ...
+    def set_site_rate_correlation(self, arg0: float) -> None:
+        ...
     def set_model_parameters(self, arg0: list[float]) -> None:
         ...
     def set_replacement_model(self, arg0: modelCode) -> None:

msasim/sailfish.py

@@ -25,14 +25,14 @@ class Distribution:
                 raise ValueError(f"Each value of the probabilities should be between 0 to 1. Received a value of {x}")
         self._dist = _Sailfish.DiscreteDistribution(dist)
     
-    def draw_sample(self) -> int:
-        return self._dist.draw_sample()
+    # def draw_sample(self) -> int:
+    #     return self._dist.draw_sample()
     
-    def set_seed(self, seed: int) -> None:
-        return self._dist.set_seed(seed)
+    # def set_seed(self, seed: int) -> None:
+    #     return self._dist.set_seed(seed)
     
-    def get_table(self) -> List:
-        return self._dist.get_table()
+    # def get_table(self) -> List:
+    #     return self._dist.get_table()
     
     def _get_Sailfish_dist(self) -> _Sailfish.DiscreteDistribution:
         return self._dist
@@ -415,7 +415,10 @@ class Simulator:
         # verify sim_protocol
         if self._verify_sim_protocol(simProtocol):
             self._simProtocol = simProtocol
-            self._simulator = _Sailfish.Simulator(self._simProtocol._sim)
+            if simulation_type == SIMULATION_TYPE.PROTEIN:
+                self._simulator = _Sailfish.AminoSimulator(self._simProtocol._sim)
+            else:
+                self._simulator = _Sailfish.NucleotideSimulator(self._simProtocol._sim)
         else:
             raise ValueError(f"failed to verify simProtocol")
         
@@ -475,7 +478,8 @@ class Simulator:
             model_parameters: List = None,
             gamma_parameters_alpha : float = 1.0,
             gamma_parameters_categories: int = 1,
-            invariant_sites_proportion: float = 0.0
+            invariant_sites_proportion: float = 0.0,
+            site_rate_correlation: float = 0.0,
         ) -> None:
         if not model:
             raise ValueError(f"please provide a substitution model from the the following list: {_Sailfish.modelCode}")
@@ -503,6 +507,8 @@ class Simulator:
 
         self._model_factory.set_gamma_parameters(gamma_parameters_alpha, gamma_parameters_categories)
         self._model_factory.set_invariant_sites_proportion(invariant_sites_proportion)
+        self._model_factory.set_site_rate_correlation(site_rate_correlation)
+
         self._simulator.init_substitution_sim(self._model_factory)
 
         self._is_sub_model_init = True
@@ -556,13 +562,11 @@ class Simulator:
             msa = Msa(blocktree._get_Sailfish_blocks(),
                         self._simProtocol._get_root(),
                         self.get_sequences_to_save())
+            self._simulator.set_aligned_sequence_map(msa._msa)
 
         # sim.init_substitution_sim(mFac)
         if self._simulation_type != SIMULATION_TYPE.NOSUBS:
-            with tempfile.TemporaryDirectory() as tmpdirname:
-                self._simulator.gen_substitutions_to_dir(msa.get_length(), tmpdirname)
-                msa._msa.set_substitutions_folder(tmpdirname)
-                msa._msa.write_msa_from_dir(str(output_file_path))
+            self._simulator.gen_substitutions_to_file(msa.get_length(), str(output_file_path))
 
 
     

{msasim-25.10.15.dist-info → msasim-25.11.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: msasim
-Version: 25.10.15
+Version: 25.11.2
 Summary: A fast MSA simulator
 Home-page: https://github.com/elyawy/Sailfish-backend
 Author: Elya Wygoda

msasim-25.11.2.dist-info/RECORD

@@ -0,0 +1,10 @@
+_Sailfish.cp36-win_amd64.pyd,sha256=vyMjXfPc30u7g5v9-fGR3JoSUKNZ8aqjRoPnTtX31-I,580608
+_Sailfish/__init__.pyi,sha256=kic4k1SjpXin4g8Ztzk8cDkMZpE8Hi-yIfkjp5g6RRI,15688
+_Sailfish/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+msasim/sailfish.py,sha256=KA-DpYKS8KpgLKrjUEOD6jPizw_P0F9LknfuzMJ8ZEM,27021
+msasim-25.11.2.dist-info/LICENSE,sha256=MgvumWWAhx44Y7XYvLMzqDUZv_Mn4nZLuC-EBl9E0l0,10483
+msasim-25.11.2.dist-info/METADATA,sha256=mTUy8gLUoa72QfuyMo8qJ7-RAreppaGjmfDJY2DBCyY,1504
+msasim-25.11.2.dist-info/WHEEL,sha256=zukbZftcRdNfJ55Q_RYV9JZ3uVyqWKyq-wDJbmszs_U,101
+msasim-25.11.2.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
+msasim-25.11.2.dist-info/RECORD,,

msasim-25.10.15.dist-info/RECORD

@@ -1,10 +0,0 @@
-_Sailfish.cp36-win_amd64.pyd,sha256=qLgUs9Q4GQHOnU3n6bdsqwUvklI08hU53T6N_2cFiFE,600064
-_Sailfish/__init__.pyi,sha256=bzuzodmX3gI7TdqWMl6UQYuIZKgY5Nnzv52xOwv4fpg,15612
-_Sailfish/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-msasim/sailfish.py,sha256=TNaryXqg5lUz7SqZdPTyY0s1fqHpvspD95yFqN7IL48,26824
-msasim-25.10.15.dist-info/LICENSE,sha256=MgvumWWAhx44Y7XYvLMzqDUZv_Mn4nZLuC-EBl9E0l0,10483
-msasim-25.10.15.dist-info/METADATA,sha256=R38IGSG20xveqWszQOJl6Kv7U0e-rHW6fuiUOTTrIFQ,1505
-msasim-25.10.15.dist-info/WHEEL,sha256=zukbZftcRdNfJ55Q_RYV9JZ3uVyqWKyq-wDJbmszs_U,101
-msasim-25.10.15.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
-msasim-25.10.15.dist-info/RECORD,,