msasim 24.9.0__tar.gz → 24.9.2__tar.gz

{msasim-24.9.0 → msasim-24.9.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: msasim
-Version: 24.9.0
+Version: 24.9.2
 Summary: A fast MSA simulator
 Home-page: https://github.com/elyawy/Sailfish-backend
 Author: Elya Wygoda

{msasim-24.9.0 → msasim-24.9.2}/msasim/sailfish.py

@@ -467,7 +467,8 @@ class Simulator:
             model: _Sailfish.modelCode,
             model_parameters: List = None,
             gamma_parameters_alpha : float = 1.0,
-            gamma_parameters_catergories: int = 1
+            gamma_parameters_catergories: 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}")
@@ -490,8 +491,9 @@ class Simulator:
                 raise ValueError(f"please provide a model parameters")
             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_invariant_sites_proportion(invariant_sites_proportion)
         self._simulator.init_substitution_sim(self._model_factory)
 
         self._is_sub_model_init = True

{msasim-24.9.0 → msasim-24.9.2}/msasim.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: msasim
-Version: 24.9.0
+Version: 24.9.2
 Summary: A fast MSA simulator
 Home-page: https://github.com/elyawy/Sailfish-backend
 Author: Elya Wygoda

{msasim-24.9.0 → msasim-24.9.2}/setup.py

@@ -9,7 +9,7 @@ from datetime import datetime
 now = datetime.now()
 
 
-__version__ = f"{now.year % 100}.{now.month+1}.0"
+__version__ = f"{now.year % 100}.{now.month+1}.2"
 
 # The main interface is through Pybind11Extension.
 # * You can add cxx_std=11/14/17, and then build_ext can be removed.

{msasim-24.9.0 → msasim-24.9.2}/src/main.cpp

@@ -123,6 +123,7 @@ PYBIND11_MODULE(_Sailfish, m) {
         .def("set_replacement_model" , &modelFactory::setReplacementModel)
         .def("set_model_parameters" , &modelFactory::setModelParameters)
         .def("set_gamma_parameters" , &modelFactory::setGammaParameters)
+        .def("set_invariant_sites_proportion", &modelFactory::setInvariantSitesProportion)
         .def("reset", &modelFactory::resetFactory);
 
 

{msasim-24.9.0 → msasim-24.9.2}/src/modelFactory.cpp

@@ -75,6 +75,7 @@ void modelFactory::setGammaParameters(MDOUBLE alpha, size_t numCategories) {
 
 void modelFactory::resetFactory() {
     _state = factoryState::ALPHABET;
+    _invariantProportion = 0.0;
 }
 
 

{msasim-24.9.0 → msasim-24.9.2}/src/rateMatrixSim.cpp

@@ -19,7 +19,8 @@
 // 	};
 
 rateMatrixSim::rateMatrixSim(modelFactory& mFac, std::shared_ptr<std::vector<bool>> nodesToSave) : 
-	_et(mFac.getTree()), _sp(mFac.getStochasticProcess()), _alph(mFac.getAlphabet()),
+	_et(mFac.getTree()), _sp(mFac.getStochasticProcess()), _alph(mFac.getAlphabet()), 
+	_invariantSitesProportion(mFac.getInvariantSitesProportion()),
 	_cpijGam(), _rootSequence(mFac.getAlphabet()), _subManager(mFac.getTree()->getNodesNum()),
 	_nodesToSave(nodesToSave), _saveRates(false), _biased_coin(0,1) {
 		// _et = mFac.getTree();
@@ -34,8 +35,12 @@ rateMatrixSim::rateMatrixSim(modelFactory& mFac, std::shared_ptr<std::vector<boo
 
 		std::vector<MDOUBLE> rateProbs;
 		for (int j = 0 ; j < _sp->categories(); ++j) {
-			rateProbs.push_back(_sp->ratesProb(j));
+			MDOUBLE currentRateProb = _sp->ratesProb(j);
+			currentRateProb = currentRateProb * (1.0  - _invariantSitesProportion);
+			rateProbs.push_back(currentRateProb);
 		}
+		if (_invariantSitesProportion > 0.0) rateProbs.push_back(_invariantSitesProportion);
+
 		_rateSampler = std::make_unique<DiscreteDistribution>(rateProbs);
 
 		std::vector<MDOUBLE> frequencies;
@@ -103,6 +108,10 @@ void rateMatrixSim::generate_substitution_log(int seqLength) {
 	for (int h = 0; h < seqLength; h++)  {
 		int selectedRandomCategory = _rateSampler->drawSample() - 1;
 		_rateCategories[h] = selectedRandomCategory;
+		if (selectedRandomCategory == _sp->categories()) {
+			ratesVec[h] = 0.0;
+			continue;
+		}
 		ratesVec[h] = _sp->rates(selectedRandomCategory);
 		sumOfRatesAcrossSites += ratesVec[h];
 	}
@@ -149,6 +158,7 @@ void rateMatrixSim::mutateEntireSeq(tree::nodeP currentNode, int seqLength) {
 
 	for (size_t site = 0; site < seqLength; ++site) {
 		ALPHACHAR parentChar = _rootSequence[site];//_subManager.getCharacter(parentId, site, _rootSequence);
+		if (_rateCategories[site] == _sp->categories()) continue;
 		ALPHACHAR nextChar = _cpijGam.getRandomChar(_rateCategories[site], nodeId, parentChar);
 		if (nextChar != parentChar){
 			_subManager.handleEvent(nodeId, site, nextChar, _rateCategories, _sp.get(), _rootSequence);