msasim 24.12.0__tar.gz → 24.13.0__tar.gz

{msasim-24.12.0 → msasim-24.13.0}/PKG-INFO

@@ -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-24.12.0 → msasim-24.13.0}/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 → msasim-24.13.0}/msasim.egg-info/PKG-INFO

@@ -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-24.12.0 → msasim-24.13.0}/src/main.cpp

@@ -113,6 +113,7 @@ PYBIND11_MODULE(_Sailfish, m) {
         .value("EX_EHO_EXP_EXT", modelCode::EX_EHO_EXP_EXT)
         .value("EX_EHO_EXP_HEL", modelCode::EX_EHO_EXP_HEL)
         .value("EX_EHO_EXP_OTH", modelCode::EX_EHO_EXP_OTH)
+        .value("CUSTOM", modelCode::CUSTOM)
         .export_values();
 
 
@@ -121,6 +122,7 @@ PYBIND11_MODULE(_Sailfish, m) {
         .def(py::init<tree*>())
         .def("set_alphabet", &modelFactory::setAlphabet)
         .def("set_replacement_model" , &modelFactory::setReplacementModel)
+        .def("set_amino_replacement_model_file" , &modelFactory::setCustomAAModelFile)
         .def("set_model_parameters" , &modelFactory::setModelParameters)
         .def("set_gamma_parameters" , &modelFactory::setGammaParameters)
         .def("set_invariant_sites_proportion", &modelFactory::setInvariantSitesProportion)

{msasim-24.12.0 → msasim-24.13.0}/src/modelFactory.cpp

@@ -30,7 +30,7 @@ void modelFactory::setReplacementModel(modelCode model) {
     _state = factoryState::PARAMETERS;
     if (_alphabet == alphabetCode::AMINOACID) _state = factoryState::GAMMA;
     if (_model == modelCode::AAJC || _model == modelCode::NUCJC) _state = factoryState::GAMMA;
-
+    if (_model == modelCode::CUSTOM) _state = factoryState::MODEL_FILE;
 }
 
 void modelFactory::setModelParameters(std::vector<MDOUBLE> params) {
@@ -63,6 +63,15 @@ void modelFactory::setModelParameters(std::vector<MDOUBLE> params) {
     _state = factoryState::GAMMA;
 }
 
+void modelFactory::setCustomAAModelFile(const std::string &fileName) {
+    if (_state!=factoryState::MODEL_FILE) {
+        std::cout << "Please set the model to 'CUSTOM' before proceeding.\n";
+        return;
+    }
+    _modelFilePath = fileName;
+    _state = factoryState::GAMMA;
+}
+
 void modelFactory::setGammaParameters(MDOUBLE alpha, size_t numCategories) {
     if (_state!=factoryState::GAMMA) {
         std::cout << "Please specify a model and its correct parameters before proceeding.\n";
@@ -184,6 +193,21 @@ std::shared_ptr<stochasticProcess> modelFactory::getStochasticProcess() {
         case modelCode::EX_EHO_EXP_OTH:
             repModel = std::make_unique<pupAll>(datMatrixHolder::EX_EHO_EXP_OTH);
             break;
+        case modelCode::CUSTOM:
+            std::ifstream in(_modelFilePath);
+            if (!in.is_open()) throw std::runtime_error("Could not open file");
+            std::stringstream contents;
+            char buffer;
+            while (in.get(buffer)) {
+                if (buffer == '\"' || buffer == '\n') continue;
+                contents << buffer;
+            }
+            in.close();
+            const std::string &tmpstr = contents.str();
+            const char* cstr = tmpstr.c_str();
+            datMatrixString aminoFileString(cstr);
+            repModel = std::make_unique<pupAll>(aminoFileString);
+            break;
     }
 
     std::unique_ptr<pijAccelerator> pij;