Support Exporting Analysis to MrBayes

.gitignore

@@ -14,6 +14,7 @@ tags
 test_scripts/iqtree_test_cmds.txt
 pllrepo/
 build/
+cmake-build-debug/
 /Default-clang
 .idea/
 .idea/codeStyleSettings.xml

alignment/alignment.cpp

@@ -23,6 +23,7 @@
 
 #include <Eigen/LU>
 #ifdef USE_BOOST
+#include <boost/bimap.hpp>
 #include <boost/math/distributions/binomial.hpp>
 #endif
 
@@ -62,6 +63,8 @@ char genetic_code23[] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSS
 char genetic_code24[] = "KNKNTTTTSSKSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"; // Pterobranchia mitochondrial
 char genetic_code25[] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSGCWCLFLF"; // Candidate Division SR1 and Gracilibacteria
 
+boost::bimap<int, char*> genetic_code_map;
+
 Alignment::Alignment()
         : vector<Pattern>()
 {
@@ -1603,7 +1606,32 @@ void Alignment::convertStateStr(string &str, SeqType seq_type) {
         (*it) = convertState(*it, seq_type);
 }
 */
-
+
+boost::bimap<int, char*> getGeneticCodeMap() {
+    if (!genetic_code_map.empty()) return genetic_code_map;
+
+    genetic_code_map.insert({1, genetic_code1});
+    genetic_code_map.insert({2, genetic_code2});
+    genetic_code_map.insert({3, genetic_code3});
+    genetic_code_map.insert({4, genetic_code4});
+    genetic_code_map.insert({5, genetic_code5});
+    genetic_code_map.insert({6, genetic_code6});
+    genetic_code_map.insert({9, genetic_code9});
+    genetic_code_map.insert({10, genetic_code10});
+    genetic_code_map.insert({11, genetic_code11});
+    genetic_code_map.insert({12, genetic_code12});
+    genetic_code_map.insert({13, genetic_code13});
+    genetic_code_map.insert({14, genetic_code14});
+    genetic_code_map.insert({16, genetic_code16});
+    genetic_code_map.insert({21, genetic_code21});
+    genetic_code_map.insert({22, genetic_code22});
+    genetic_code_map.insert({23, genetic_code23});
+    genetic_code_map.insert({24, genetic_code24});
+    genetic_code_map.insert({25, genetic_code25});
+
+    return genetic_code_map;
+}
+
 void Alignment::initCodon(char *gene_code_id) {
     // build index from 64 codons to non-stop codons
 	int transl_table = 1;
@@ -1613,30 +1641,13 @@ void Alignment::initCodon(char *gene_code_id) {
 		} catch (string &str) {
 			outError("Wrong genetic code ", gene_code_id);
 		}
-		switch (transl_table) {
-		case 1: genetic_code = genetic_code1; break;
-		case 2: genetic_code = genetic_code2; break;
-		case 3: genetic_code = genetic_code3; break;
-		case 4: genetic_code = genetic_code4; break;
-		case 5: genetic_code = genetic_code5; break;
-		case 6: genetic_code = genetic_code6; break;
-		case 9: genetic_code = genetic_code9; break;
-		case 10: genetic_code = genetic_code10; break;
-		case 11: genetic_code = genetic_code11; break;
-		case 12: genetic_code = genetic_code12; break;
-		case 13: genetic_code = genetic_code13; break;
-		case 14: genetic_code = genetic_code14; break;
-		case 15: genetic_code = genetic_code15; break;
-		case 16: genetic_code = genetic_code16; break;
-		case 21: genetic_code = genetic_code21; break;
-		case 22: genetic_code = genetic_code22; break;
-		case 23: genetic_code = genetic_code23; break;
-		case 24: genetic_code = genetic_code24; break;
-		case 25: genetic_code = genetic_code25; break;
-		default:
+		auto codeMap = getGeneticCodeMap();
+		auto found = codeMap.left.find(transl_table);
+		if (found == codeMap.left.end()) {
 			outError("Wrong genetic code ", gene_code_id);
-			break;
+			return;
 		}
+		genetic_code = found->second;
 	} else {
 		genetic_code = genetic_code1;
 	}
@@ -1669,6 +1680,15 @@ void Alignment::initCodon(char *gene_code_id) {
 //	cout << "num_states = " << num_states << endl;
 }
 
+int Alignment::getGeneticCodeId() {
+    if (seq_type != SEQ_CODON || genetic_code == nullptr) return 0;
+
+    auto code_map = getGeneticCodeMap();
+    auto found = code_map.right.find(genetic_code);
+    if (found == code_map.right.end()) return 0;
+    return found->second;
+}
+
 int getMorphStates(StrVector &sequences) {
 	char maxstate = 0;
 	for (StrVector::iterator it = sequences.begin(); it != sequences.end(); it++)

alignment/alignment.h

@@ -1010,6 +1010,12 @@ class Alignment : public vector<Pattern>, public CharSet, public StateSpace {
      */
     void extractMapleFile(const std::string& aln_name, const InputType& format);
 
+    /**
+     * Get the numerical id of the genetic code
+     * @return id the genetic code id, or 0 if not a codon type
+     */
+    int getGeneticCodeId();
+
 protected:
 
 

main/phyloanalysis.cpp

@@ -1156,6 +1156,12 @@ void printOutfilesInfo(Params &params, IQTree &tree) {
     if (params.optimize_linked_gtr) {
         cout << "  GTRPMIX nex file:              " << params.out_prefix << ".GTRPMIX.nex" << endl;
     }
+
+    if (params.mr_bayes_output) {
+        cout << endl << "MrBayes block written to:" << endl;
+        cout << "  Base template file:            " << params.out_prefix << ".mr_bayes_scheme.nex" << endl;
+        cout << "  Template file with parameters: " << params.out_prefix << ".mr_bayes_model.nex" << endl;
+    }
     cout << endl;
 
 }
@@ -2596,6 +2602,92 @@ void printTrees(vector<string> trees, Params &params, string suffix) {
     treesOut.close();
 }
 
+void printMrBayesBlockFile(const char* filename, IQTree* &iqtree, bool inclParams) {
+    ofstream out;
+    try {
+        out.exceptions(ios::failbit | ios::badbit);
+        out.open(filename);
+
+        string provide = "basic models";
+        if (inclParams) provide = "optimized values";
+        else if (iqtree->isSuperTree()) provide = "basic partition structure and models";
+
+        // Write Warning
+        out << "#nexus" << endl << endl
+            <<"[This MrBayes Block Declaration provides the " << provide << " from the IQTree Run.]" << endl
+            << "[Note that MrBayes does not support a large collection of models, so defaults of 'nst=6' for DNA and 'wag' for Protein will be used if a model that does not exist in MrBayes is used.]" << endl;
+
+        if (inclParams)
+            out << "[However, for those cases, there will still be a rate matrix provided.]" << endl
+                << "[For DNA, this will still mean the rates may vary outside the restrictions of the model.]" << endl
+                << "[For Protein, this is essentially a perfect replacement.]" << endl;
+
+        out << "[Furthermore, the Model Parameter '+R' will be replaced by '+G'.]" << endl
+            << "[This should be used as a Template Only.]" << endl << endl;
+
+        // Begin File, Print Charsets
+        out << "begin mrbayes;" << endl;
+    } catch (ios::failure &) {
+        outError(ERR_WRITE_OUTPUT, filename);
+    }
+
+    if (!iqtree->isSuperTree()) {
+        // Set Outgroup (if available)
+        if (!iqtree->rooted) out << "  outgroup " << iqtree->root->name << ";" << endl << endl;
+
+        out << "  [Using Model '" << iqtree->getModelName() << "']" << endl;
+        iqtree->getModel()->printMrBayesModelText(out, "all", "", false, inclParams);
+
+        out << endl << "end;" << endl;
+        out.close();
+        return;
+    }
+
+    auto superTree = (PhyloSuperTree*) iqtree;
+    auto saln = (SuperAlignment*) superTree->aln;
+    auto size = superTree->size();
+
+    for (int part = 0; part < size; part++) {
+        string name = saln->partitions[part]->name;
+        replace(name.begin(), name.end(), '+', '_');
+        out << "  charset " << name << " = ";
+
+        string pos = saln->partitions[part]->position_spec;
+        replace(pos.begin(), pos.end(), ',' , ' ');
+        out << pos << ";" << endl;
+    }
+
+    // Create Partition
+    out << endl << "  partition iqtree = " << size << ": ";
+    for (int part = 0; part < size; part++) {
+        if (part != 0) out << ", ";
+
+        string name = saln->partitions[part]->name;
+        replace(name.begin(), name.end(), '+', '_');
+        out << name;
+    }
+    out << ";" << endl;
+
+    // Set Partition for Use
+    out << "  set partition = iqtree;" << endl;
+
+    // Set Outgroup (if available)
+    if (!superTree->rooted) out << "  outgroup " << superTree->root->name << ";" << endl << endl;
+
+    // Partition-Specific Model Information
+    for (int part = 0; part < size; part++) {
+        PhyloTree* currentTree = superTree->at(part);
+
+        // MrBayes Partitions are 1-indexed
+        out << "  [Partition No. " << convertIntToString(part + 1) << ", Using Model '" << currentTree->getModelName() << "']" << endl;
+        currentTree->getModel()->printMrBayesModelText(out,
+                convertIntToString(part + 1), saln->partitions[part]->name, true, inclParams);
+        out << endl;
+    }
+    out << "end;" << endl;
+    out.close();
+}
+
 /************************************************************
  *  MAIN TREE RECONSTRUCTION
  ***********************************************************/
@@ -3100,8 +3192,15 @@ void runTreeReconstruction(Params &params, IQTree* &iqtree) {
 
     }
     if (iqtree->isSuperTree()) {
-        ((PhyloSuperTree*) iqtree)->computeBranchLengths();
-        ((PhyloSuperTree*) iqtree)->printBestPartitionParams((string(params.out_prefix) + ".best_model.nex").c_str());
+        auto superTree = (PhyloSuperTree*) iqtree;
+        superTree->computeBranchLengths();
+        superTree->printBestPartitionParams((string(params.out_prefix) + ".best_model.nex").c_str());
+    }
+    if (params.mr_bayes_output) {
+        cout << endl << "Writing MrBayes Block Files..." << endl;
+        printMrBayesBlockFile((string(params.out_prefix) + ".mr_bayes_scheme.nex").c_str(), iqtree, false);
+        printMrBayesBlockFile((string(params.out_prefix) + ".mr_bayes_model.nex").c_str(), iqtree, true);
+        cout << endl;
     }
 
     cout << "BEST SCORE FOUND : " << iqtree->getCurScore() << endl;

main/phylotesting.h

@@ -390,5 +390,12 @@ string convertSeqTypeToSeqTypeName(SeqType seq_type);
 
 string detectSeqTypeName(string model_name);
 
+/**
+ * get string name from a SeqType object
+ * @param seq_type input sequence type
+ * @return name
+ */
+string getSeqTypeName(SeqType seq_type);
+
 
 #endif /* PHYLOTESTING_H_ */

model/modelbin.cpp

@@ -76,3 +76,58 @@ string ModelBIN::getNameParams(bool show_fixed_params) {
     }
     return retname.str();
 }
+
+void ModelBIN::printMrBayesModelText(ofstream& out, string partition, string charset, bool isSuperTree, bool inclParams) {
+    RateHeterogeneity* rate = phylo_tree->getRate();
+
+    // MrBayes does not support Invariable Modifier for Binary data
+    if (rate->isFreeRate() || rate->getPInvar() > 0.0) {
+        warnLogStream("MrBayes does not support Invariable Sites with Binary Data! +I has been ignored!", out);
+    }
+
+    // Lset Parameters
+    out << "  lset applyto=(" << partition << ") rates=";
+
+    // Free Rate should be substituted by +G (+I not supported)
+    bool hasGamma = rate->getGammaShape() != 0.0 || rate->isFreeRate();
+    if (hasGamma) {
+        // Rate Categories + Gamma
+        out << "gamma ngammacat=" << rate->getNRate();
+    } else
+        out << "equal";
+
+    out << ";" << endl;
+
+    if (!inclParams) {
+        if (freq_type == FREQ_EQUAL) out << "  prset applyto=(" << partition << ") statefreqpr=fixed(equal);" << endl;
+        return;
+    }
+
+    // Prset Parameters
+    out << "  prset applyto=(" << partition << ")";
+
+    // Freerate (+R)
+    // Get replacement Gamma Shape
+    if (rate->isFreeRate()) {
+        printMrBayesFreeRateReplacement(rate, charset, out, false);
+    }
+
+    // Gamma Distribution (+G/+R)
+    // Dirichlet is not available here, use fixed
+    if (rate->getGammaShape() > 0.0)
+        out << " shapepr=fixed(" << minValueCheckMrBayes(rate->getGammaShape()) << ")";
+
+    // State Frequencies
+    if (freq_type == FREQ_EQUAL)
+        out << " statefreqpr=fixed(equal)";
+    else {
+        out << " statefreqpr=dirichlet(";
+        for (int i = 0; i < num_states; ++i) {
+            if (i != 0) out << ", ";
+            out << minValueCheckMrBayes(state_freq[i]);
+        }
+        out << ")";
+    }
+
+    out << ";" << endl;
+}

model/modelbin.h

@@ -55,6 +55,18 @@ class ModelBIN : public ModelMarkov
     */
     virtual void startCheckpoint();
 
+    /**
+     * Print the model information in a format that can be accepted by MrBayes, using lset and prset.<br>
+     * By default, it simply prints a warning to the log and to the stream, stating that this model is not supported by MrBayes.
+     * @param rate the rate information
+     * @param out the ofstream to print the result to
+     * @param partition the partition to apply lset and prset to
+     * @param charset the current partition's charset. Useful for getting information from the checkpoint file
+     * @param isSuperTree whether the tree is a super tree. Useful for retrieving information from the checkpoint file, which has different locations for PhyloTree and PhyloSuperTree
+     * @param inclParams whether to include IQTree optimized parameters for the model
+     */
+    virtual void printMrBayesModelText(ofstream& out, string partition, string charset, bool isSuperTree, bool inclParams);
+
 };
 
 #endif