msasim 24.8.1__tar.gz → 24.9.0__tar.gz

{msasim-24.8.1 → msasim-24.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: msasim
-Version: 24.8.1
+Version: 24.9.0
 Summary: A fast MSA simulator
 Home-page: https://github.com/elyawy/Sailfish-backend
 Author: Elya Wygoda

{msasim-24.8.1 → msasim-24.9.0}/msasim/sailfish.py

@@ -10,6 +10,7 @@ from enum import Enum
 MODEL_CODES = _Sailfish.modelCode
 
 class SIMULATION_TYPE(Enum):
+    NOSUBS = 0
     DNA = 1
     PROTEIN = 2
 
@@ -413,13 +414,15 @@ class Simulator:
             raise ValueError(f"failed to verify simProtocol")
         
         if not simulation_type:
-            warnings.warn(f"simulation type not provided -> running protein simulation")
-            simulation_type = SIMULATION_TYPE.PROTEIN
+            warnings.warn(f"simulation type not provided -> running indel only simulation")
+            simulation_type = SIMULATION_TYPE.NOSUBS
         
         if simulation_type == SIMULATION_TYPE.PROTEIN:
             self._alphabet = _Sailfish.alphabetCode.AMINOACID
         elif simulation_type == SIMULATION_TYPE.DNA:
             self._alphabet = _Sailfish.alphabetCode.NUCLEOTIDE
+        elif simulation_type == SIMULATION_TYPE.NOSUBS:
+            self._alphabet = _Sailfish.alphabetCode.NULLCODE
         else:
             raise ValueError(f"unknown simulation type, please provde one of the following: {[e.name for e in SIMULATION_TYPE]}")
         
@@ -525,8 +528,9 @@ class Simulator:
                           self.get_sequences_to_save())
 
             # sim.init_substitution_sim(mFac)
-            substitutions = self.gen_substitutions(msa.get_length())
-            msa.fill_substitutions(substitutions)
+            if self._simulation_type != SIMULATION_TYPE.NOSUBS:
+                substitutions = self.gen_substitutions(msa.get_length())
+                msa.fill_substitutions(substitutions)
 
             Msas.append(msa)
         return Msas

{msasim-24.8.1 → msasim-24.9.0}/msasim.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: msasim
-Version: 24.8.1
+Version: 24.9.0
 Summary: A fast MSA simulator
 Home-page: https://github.com/elyawy/Sailfish-backend
 Author: Elya Wygoda

{msasim-24.8.1 → msasim-24.9.0}/setup.py

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

{msasim-24.8.1 → msasim-24.9.0}/src/main.cpp

@@ -2,7 +2,7 @@
 
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
-
+#include <memory>
 
 #include "./Simulator.h"
 
@@ -80,6 +80,7 @@ PYBIND11_MODULE(_Sailfish, m) {
         .def(py::init<>());
 
     py::enum_<alphabetCode>(m, "alphabetCode")
+        .value("NULLCODE", alphabetCode::NULLCODE)
         .value("NUCLEOTIDE", alphabetCode::NUCLEOTIDE)
         .value("AMINOACID", alphabetCode::AMINOACID)
         .export_values();
@@ -140,8 +141,8 @@ PYBIND11_MODULE(_Sailfish, m) {
 
 
     py::class_<MSA>(m, "Msa")
-        .def(py::init<size_t, size_t, const std::vector<bool>&>())
-        .def(py::init<BlockMap, tree::TreeNode*, const std::vector<bool>&>())
+        .def(py::init<size_t, size_t, const std::vector<bool>& >())
+        .def(py::init<BlockMap, tree::TreeNode*, const std::vector<bool>& >())
         .def("generate_msas", &MSA::generateMSAs)
         .def("length", &MSA::getMSAlength)
         .def("num_sequences", &MSA::getNumberOfSequences)

{msasim-24.8.1 → msasim-24.9.0}/src/rateMatrixSim.cpp

@@ -18,14 +18,13 @@
 // 	_et(_inEt), _sp(sp),_alph(alph),_avgSubtitutionsPerSite(0.0) {
 // 	};
 
-rateMatrixSim::rateMatrixSim(modelFactory& mFac) : 
+rateMatrixSim::rateMatrixSim(modelFactory& mFac, std::shared_ptr<std::vector<bool>> nodesToSave) : 
 	_et(mFac.getTree()), _sp(mFac.getStochasticProcess()), _alph(mFac.getAlphabet()),
 	_cpijGam(), _rootSequence(mFac.getAlphabet()), _subManager(mFac.getTree()->getNodesNum()),
-	_nodesToSave(_et->getNodesNum(), false), _saveRates(false), _biased_coin(0,1) {
+	_nodesToSave(nodesToSave), _saveRates(false), _biased_coin(0,1) {
 		// _et = mFac.getTree();
 		// _sp = mFac.getStochasticProcess();
 		// _alph = mFac.getAlphabet();
-		setSaveStateLeaves(_et->getRoot());
 
 		size_t alphaSize = _sp->alphabetSize();
 
@@ -49,13 +48,6 @@ rateMatrixSim::rateMatrixSim(modelFactory& mFac) :
 
 };
 
-void rateMatrixSim::setSaveStateLeaves(const tree::nodeP &node) {
-	for(auto &node: node->getSons()) {
-		if (node->isLeaf()) _nodesToSave[node->id()] = true;
-		setSaveStateLeaves(node);
-	}
-}
-
 void rateMatrixSim::setSaveRates(bool saveRates) {
 	_saveRates = saveRates;
 }
@@ -120,7 +112,7 @@ void rateMatrixSim::generate_substitution_log(int seqLength) {
 	// _siteSampler = std::make_unique<DiscreteDistribution>(ratesVec, sumOfRatesNoramlizingFactor);
 	_rootSequence.resize(seqLength);
 	generateRootSeq(seqLength, ratesVec);
-	if (_nodesToSave[_et->getRoot()->id()]) saveSequence(_et->getRoot()->id(), _et->getRoot()->name());
+	if ((*_nodesToSave)[_et->getRoot()->id()]) saveSequence(_et->getRoot()->id(), _et->getRoot()->name());
 
 	mutateSeqRecuresively(_et->getRoot(), seqLength);
 	_subManager.clear();
@@ -131,7 +123,7 @@ void rateMatrixSim::mutateSeqRecuresively(tree::nodeP currentNode, int seqLength
 
 	for (auto &node: currentNode->getSons()) {
 		mutateSeqAlongBranch(node, seqLength);
-		if (_nodesToSave[node->id()]) saveSequence(node->id(), node->name());
+		if ((*_nodesToSave)[node->id()]) saveSequence(node->id(), node->name());
 		mutateSeqRecuresively(node, seqLength);
 
 		if (!_subManager.isEmpty(currentNode->id())) {
@@ -253,35 +245,6 @@ std::unique_ptr<sequenceContainer> rateMatrixSim::getSequenceContainer() {
 	return std::move(outputSequences);
 }
 
-void rateMatrixSim::setNodesToSave(std::vector<size_t> nodeIDs) {
-	std::fill(_nodesToSave.begin(), _nodesToSave.end(), false);
-	for(auto &nodeID: nodeIDs) {
-		_nodesToSave[nodeID] = true;
-	}
-}
-
-void rateMatrixSim::setSaveAllNodes() {
-	for (size_t i = 0; i < _nodesToSave.size(); i++) {
-		_nodesToSave[i] = true;
-	}
-}
-
-void rateMatrixSim::setSaveRoot() {
-	_nodesToSave[0] = true;
-}
-
-
-void rateMatrixSim::changeNodeSaveState(size_t nodeID) {
-	_nodesToSave[nodeID] = !_nodesToSave[nodeID];
-}
-
-bool rateMatrixSim::getNodeSaveState(size_t nodeID) {
-	return _nodesToSave[nodeID];
-}
-
-const std::vector<bool>& rateMatrixSim::getNodesSaveList() {
-	return _nodesToSave;
-}
 
 bool rateMatrixSim::testSumOfRates() {
 	MDOUBLE sumOfRates = 0.0;