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141 lines
3.7 KiB
C++
141 lines
3.7 KiB
C++
// $Id: distances.cpp 674 2006-04-09 17:06:42Z ninio $
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#include "tree.h"
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#include "sequenceContainer.h"
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#include "mainSemphy.h"
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#include "njGamma.h"
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#include "logFile.h"
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#include "treeUtil.h"
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#include "likeDist.h"
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#include "someUtil.h"
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#include "codon.h"
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#include "recognizeFormat.h"
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#include "pDistance.h"
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#include "jcDistance.h"
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#include "likeDist.h"
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#include <iostream>
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#include <cassert>
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using namespace std;
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int main(int argc,char* argv[]) {
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if (argc < 2) errorMsg::reportError("The program must get some parameters in the command line, use -h for help");
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semphy_args_info args_info;
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if (semphy_cmdline_parser(argc, argv, &args_info) != 0) {
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errorMsg::reportError("error reading command line",1);
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}
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if (args_info.inputs_num<1)
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errorMsg::reportError("Need a file with an extra pair of sequances",1);
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// check that we have all we need:
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if (!args_info.tree_given) {
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errorMsg::reportError("Must enter input tree",1);
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}
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if (!args_info.alpha_given) {
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errorMsg::reportError("Must set gamma",1);
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}
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mainSemphy ms(args_info);
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// see that we actually got gamma
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assert(ms.getStochasticProcess().categories() >1);
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for (int i=0;i<ms.getStochasticProcess().categories();++i)
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LOG(3,<<"category["<<i<<"]="<<ms.getStochasticProcess().rates(i)<<"\t"<<ms.getStochasticProcess().ratesProb(i)<<endl);
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if (args_info.likelihood_flag)
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ms.computeLikelihoodAndLikelihoodPerPosition();
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else
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ms.optimizeBranchLengths(); // this will do both bbl and alpha.
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ms.printLikelihoodAndLikelihoodPerPosition();
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ms.printTree();
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VVdouble posteriorProbVV; // pos * rate
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ms.extractPosteriorProb(posteriorProbVV);
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LOGDO(3, ms.out()<<posteriorProbVV<<endl);
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// read the extra sequances
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sequenceContainer sc;
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alphabet* alphP=NULL;
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switch (args_info.alphabet_arg)
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{ // allwayes defined, with default
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case 4:
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alphP = new nucleotide;
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break;
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case 20:
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alphP = new amino;
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break;
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case 64:
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alphP = new codon;
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break;
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default: errorMsg::reportError("error getting the alphabet");
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}
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if (args_info.categories_given)
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LOG(3,<<"using "<<args_info.categories_arg<<" bins for gamma"<<endl);
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if (args_info.inputs_num <1)
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errorMsg::reportError("please provide a file with a list of sequnce pair files");
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ifstream seqlist;
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seqlist.open(args_info.inputs[0]);
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if (! seqlist.good())
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errorMsg::reportError("can not open sequence pair list file");
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char tmp[1000]; // this is not ideal!
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while (!seqlist.eof()){
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seqlist >> tmp;
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if (seqlist.eof()) break;
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string seqid(tmp);
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ms.out() << seqid <<"\t";
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seqlist >> tmp;
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string sequenceFileName(tmp);
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ms.out() << sequenceFileName<<"\t";
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ifstream ins;
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ins.open(sequenceFileName.c_str());
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if (! ins.good())
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errorMsg::reportError("can not open sequence pair file");
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sc = recognizeFormat::read(ins,alphP);
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ins.close();
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jcDistance jcD(args_info.alphabet_arg);
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ms.out() <<""<<jcD.giveDistance(sc[0], sc[1], NULL)<<"\t";
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pDistance pD;
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ms.out() <<""<<pD.giveDistance(sc[0], sc[1], NULL)<<"\t";
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pupAll probMod(datMatrixHolder::dayhoff);
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chebyshevAccelerator pijAcc(&probMod);
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uniDistribution dist1;
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stochasticProcess sp1(&dist1, &pijAcc);
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likeDist lD1(sp1);
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ms.out() <<""<<lD1.giveDistance(sc[0], sc[1], NULL)<<"\t";
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gammaDistribution dist2(args_info.gamma_arg,args_info.categories_arg);
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stochasticProcess sp2 = ms.getStochasticProcess();
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likeDist lD2(sp2);
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ms.out() <<""<<lD2.giveDistance(sc[0], sc[1], NULL)<<"\t";
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gammaMLDistances lD3(sp2,posteriorProbVV);
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ms.out() <<""<<lD3.giveDistance(sc[0], sc[1], NULL)<<endl;
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}
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delete alphP;
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return 0;
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}
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