msasim 24.12.0__cp37-cp37m-musllinux_1_2_x86_64.whl → 24.13.0__cp37-cp37m-musllinux_1_2_x86_64.whl

msasim/sailfish.py

@@ -462,15 +462,16 @@ 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 +479,8 @@ 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 +492,7 @@ 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-24.13.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: msasim
-Version: 24.12.0
+Version: 24.13.0
 Summary: A fast MSA simulator
 Home-page: https://github.com/elyawy/Sailfish-backend
 Author: Elya Wygoda

msasim-24.13.0.dist-info/RECORD

@@ -0,0 +1,10 @@
+_Sailfish.cpython-37m-x86_64-linux-gnu.so,sha256=pQ8CIAnuGyaRWK4Se192LSpmDcQK_pfgxSDwPJCwX2c,1381761
+msasim.libs/libstdc++-496613c0.so.6.0.32,sha256=AwZhL5WFT99I2Q6vIxXOhW7qddfuOZ1xecxiP9QTVY4,3494361
+msasim.libs/libgcc_s-a3a07607.so.1,sha256=5ptIUeAzZweNZrFehN0_Bb5B0FcJgux7NbAFoU8vwwo,148041
+msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+msasim/sailfish.py,sha256=o_6N1f1rFXgG0z_b17CJRC3wUzIcoKy__c6s1FroHgI,25901
+msasim-24.13.0.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
+msasim-24.13.0.dist-info/RECORD,,
+msasim-24.13.0.dist-info/LICENSE,sha256=p1Aa_mM2Nu6dG3XqMVU62Jhf04lNOwtXUrhhvhcDips,10312
+msasim-24.13.0.dist-info/METADATA,sha256=mIMhgdJG3uQw8b9JZZIIc84JVcOtnrMFK_WiHo9zwIo,1468
+msasim-24.13.0.dist-info/WHEEL,sha256=q5rUVfD8JDL5S3yQAj8GHnejX-TLAuJehhTULM4SQNo,112

msasim-24.12.0.dist-info/RECORD

@@ -1,10 +0,0 @@
-_Sailfish.cpython-37m-x86_64-linux-gnu.so,sha256=ZChaJO6q20jJQPvPhRaTP_YVt2h_hn1otOKU17wOhwk,1373513
-msasim-24.12.0.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
-msasim-24.12.0.dist-info/RECORD,,
-msasim-24.12.0.dist-info/LICENSE,sha256=p1Aa_mM2Nu6dG3XqMVU62Jhf04lNOwtXUrhhvhcDips,10312
-msasim-24.12.0.dist-info/METADATA,sha256=jVxAKL5akbzugkbsmgzPnFcQ2_kc84Pu18k0V4d1_bE,1468
-msasim-24.12.0.dist-info/WHEEL,sha256=q5rUVfD8JDL5S3yQAj8GHnejX-TLAuJehhTULM4SQNo,112
-msasim.libs/libstdc++-496613c0.so.6.0.32,sha256=AwZhL5WFT99I2Q6vIxXOhW7qddfuOZ1xecxiP9QTVY4,3494361
-msasim.libs/libgcc_s-a3a07607.so.1,sha256=5ptIUeAzZweNZrFehN0_Bb5B0FcJgux7NbAFoU8vwwo,148041
-msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-msasim/sailfish.py,sha256=I45ufK0owZIsu7zOBN427rQ07RGl3Jll8mnGiCS0Ufo,25698