msasim 24.12.0__cp36-cp36m-win_amd64.whl → 25.3.0__cp36-cp36m-win_amd64.whl

msasim/sailfish.py

@@ -218,6 +218,7 @@ class SimProtocol:
                  insertion_rate: float = 0.0,
                  deletion_dist: Distribution = ZipfDistribution(1.7, 50),
                  insertion_dist: Distribution = ZipfDistribution(1.7, 50),
+                 minimum_seq_size: int = 100,
                  seed: int = 0,
         ):
         if isinstance(tree, Tree):
@@ -237,7 +238,8 @@ class SimProtocol:
         self.set_insertion_rates(insertion_rate=insertion_rate)
         self.set_deletion_length_distributions(deletion_dist=deletion_dist)
         self.set_insertion_length_distributions(insertion_dist=insertion_dist)
-    
+        self.set_min_sequence_size(min_sequence_size=minimum_seq_size)
+
     def get_tree(self) -> Tree:
         return self._tree
     
@@ -264,6 +266,11 @@ class SimProtocol:
     def get_sequence_size(self) -> int:
         return self._root_seq_size
     
+    def set_min_sequence_size(self, min_sequence_size: int) -> None:
+        self._sim.set_minimum_sequence_size(min_sequence_size)
+        self._min_seq_size = min_sequence_size
+
+    
     def set_insertion_rates(self, insertion_rate: Optional[float] = None, insertion_rates: Optional[List[float]] = None) -> None:
         if insertion_rate is not None:
             self.insertion_rates = [insertion_rate] * self._num_branches
@@ -462,15 +469,16 @@ class Simulator:
     def set_replacement_model(
             self,
             model: _Sailfish.modelCode,
+            amino_model_file: pathlib.Path = None,
             model_parameters: List = None,
             gamma_parameters_alpha : float = 1.0,
-            gamma_parameters_catergories: int = 1,
+            gamma_parameters_categories: int = 1,
             invariant_sites_proportion: float = 0.0
         ) -> None:
         if not model:
             raise ValueError(f"please provide a substitution model from the the following list: {_Sailfish.modelCode}")
-        if int(gamma_parameters_catergories) != gamma_parameters_catergories:
-            raise ValueError(f"gamma_parameters_catergories has to be a positive int value: received value of {gamma_parameters_catergories}")
+        if int(gamma_parameters_categories) != gamma_parameters_categories:
+            raise ValueError(f"gamma_parameters_catergories has to be a positive int value: received value of {gamma_parameters_categories}")
         self._model_factory = _Sailfish.modelFactory(self._simProtocol._get_Sailfish_tree())
 
         self._model_factory.set_alphabet(self._alphabet)
@@ -478,6 +486,8 @@ class Simulator:
             if model_parameters:
                 raise ValueError(f"no model parameters are used in protein, recevied value of: {model_parameters}")
             self._model_factory.set_replacement_model(model)
+            if model == MODEL_CODES.CUSTOM and amino_model_file:
+                self._model_factory.set_amino_replacement_model_file(str(amino_model_file))
         else:
             if model == MODEL_CODES.NUCJC and model_parameters:
                 raise ValueError(f"no model parameters in JC model, recevied value of: {model_parameters}")
@@ -489,7 +499,7 @@ class Simulator:
             else:
                 self._model_factory.set_model_parameters(model_parameters)
 
-        self._model_factory.set_gamma_parameters(gamma_parameters_alpha, gamma_parameters_catergories)
+        self._model_factory.set_gamma_parameters(gamma_parameters_alpha, gamma_parameters_categories)
         self._model_factory.set_invariant_sites_proportion(invariant_sites_proportion)
         self._simulator.init_substitution_sim(self._model_factory)
 

{msasim-24.12.0.dist-info → msasim-25.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: msasim
-Version: 24.12.0
+Version: 25.3.0
 Summary: A fast MSA simulator
 Home-page: https://github.com/elyawy/Sailfish-backend
 Author: Elya Wygoda

msasim-25.3.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+_Sailfish.cp36-win_amd64.pyd,sha256=DaOu0oYFnxGlAMemnn2lxLXdW56KCQNKpB3uWIFyUOY,627712
+msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+msasim/sailfish.py,sha256=ex2EX4xSuxs6D8iBZk4ar8CjPcjWyJm2uewfk7jGJ-A,26772
+msasim-25.3.0.dist-info/LICENSE,sha256=MgvumWWAhx44Y7XYvLMzqDUZv_Mn4nZLuC-EBl9E0l0,10483
+msasim-25.3.0.dist-info/METADATA,sha256=8r6prqtfuwnoPydw8dKwx6oCKeLgG_Ib_pFmYOsdlhE,1503
+msasim-25.3.0.dist-info/WHEEL,sha256=zukbZftcRdNfJ55Q_RYV9JZ3uVyqWKyq-wDJbmszs_U,101
+msasim-25.3.0.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
+msasim-25.3.0.dist-info/RECORD,,

msasim-24.12.0.dist-info/RECORD

@@ -1,8 +0,0 @@
-_Sailfish.cp36-win_amd64.pyd,sha256=tbAcQNnnxQwyr0wJ-taaSo_rmSE6_WPvaBlX27PNGnw,622592
-msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-msasim/sailfish.py,sha256=ElArIFObfW_1qc8no5Q0DKqTDwuF15lFibEVV0wUqzM,26261
-msasim-24.12.0.dist-info/LICENSE,sha256=MgvumWWAhx44Y7XYvLMzqDUZv_Mn4nZLuC-EBl9E0l0,10483
-msasim-24.12.0.dist-info/METADATA,sha256=JhV_cW2pVAlg6BLm_KV_YMVo2zdZbL4FcxtdFC_fWJI,1504
-msasim-24.12.0.dist-info/WHEEL,sha256=zukbZftcRdNfJ55Q_RYV9JZ3uVyqWKyq-wDJbmszs_U,101
-msasim-24.12.0.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
-msasim-24.12.0.dist-info/RECORD,,