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homer.C
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homer.C
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/****************************************************************
HOMER : Higher-Order Markovian Eukaryotic Recognizer
A simple HMM for demonstrating HMM training & decoding algorithms
(named in honor of the great Homer Simpson)
bmajoros@tigr.org
Copyright (c)2004, Bill Majoros. This software is governed by
the ARTISTIC LICENSE (see www.opensource.org).
****************************************************************/
#include <string>
#include <iostream>
#include <math.h>
#include <fstream>
#include "tigr++/TigrCommandLine.H"
#include "tigr++/TigrSet.H"
#include "tigr++/TigrRegex.H"
#include "tigr++/TigrVector.H"
#include "tigr++/TigrMap.H"
#include "FastViterbi.H"
#include "tigr++/TigrFastaReader.H"
#include "tigr++/TigrFile.H"
#include "tigr++/DnaAlphabet.H"
#include "tigr++/NthOrderStringIterator.H"
#include "HigherOrderAlphabet.H"
using namespace std;
class Exon
{
int begin, end, transcriptId;
TigrString axisId;
char strand;
public:
Exon(int begin,int end,int transcriptId,TigrString axisId,char strand)
: begin(begin), end(end), transcriptId(transcriptId), axisId(axisId),
strand(strand) {}
void printOn(ostream &);
int getTranscriptId() const {return transcriptId;}
char getStrand() const {return strand;}
};
ostream &operator<<(ostream &,Exon &);
class Application
{
DnaAlphabet alphabet;
HigherOrderAlphabet *higherOrderAlphabet;
TigrSet<int> exonStates, intergenicStates;
TigrRegex deflineRegex;
vector<HiddenMarkovModel*> submodels;
int numSymbols;
vector<int> submodelOrigins; // state ids in composite HMM
int numSubmodels;
TigrVector<Exon*> exons;
TigrMap<int,int> exonsPerGene;
int order;
void addToSet(TigrSet<int> &,int fromState,int numStates);
void loadSubmodels(const TigrString &filename);
HiddenMarkovModel *loadHMM(const TigrString &);
void produceOutput();
double getPathScore(vector<int> &path,Sequence &,HiddenMarkovModel &);
public:
Application();
int main(int argc,char *argv[]);
};
int main(int argc,char *argv[])
{
try
{
Application app;
return app.main(argc,argv);
}
catch(const char *p)
{
cerr << p << endl;
}
catch(const string &msg)
{
cerr << msg.c_str() << endl;
}
catch(const exception &e)
{
cerr << "STL exception caught in main:\n" << e.what() << endl;
}
catch(...)
{
cerr << "Unknown exception caught in main" << endl;
}
return -1;
}
Application::Application()
: deflineRegex(">\\s*(\\S+)")
{
// ctor
}
int Application::main(int argc,char *argv[])
{
// Process command line
TigrCommandLine cmd(argc,argv,"");
if(cmd.numArgs()!=3)
throw string("homer [-p] <*.hmm> <submodels.txt> <*.fasta>\n");
TigrString hmmFilename=cmd.arg(0);
TigrString submodelsFilename=cmd.arg(1);
TigrString fastaFilename=cmd.arg(2);
time_t t=time(NULL);
loadSubmodels(submodelsFilename);
HiddenMarkovModel &hmm=*loadHMM(hmmFilename);
FastViterbi viterbi(hmm);
order=hmm.getOrder();
higherOrderAlphabet=new HigherOrderAlphabet(alphabet,order);
TigrFastaReader fastaReader(fastaFilename);
TigrString defline, sequence;
int transcriptId=0;
while(fastaReader.nextSequence(defline,sequence))
{
if(!deflineRegex.search(defline))
throw TigrString("bad defline: ")+defline;
TigrString axisId=deflineRegex[1];
Sequence seq(sequence,alphabet);
TigrArray2D<int> ngramArray(seq.getLength(),order+1);
higherOrderAlphabet->initNgramArray(ngramArray,sequence);
double pathScore;
vector<int> &path=*viterbi.getPath(ngramArray,pathScore);
int len=path.size();
int exonBegin=-1;
bool inExon=false, inIntergenic=false;
for(int i=0 ; i<len ; ++i)
{
int state=path[i];
if(!inExon && exonStates.isMember(state))
{
if(inIntergenic)
{
inIntergenic=false;
++transcriptId;
}
inExon=true;
exonBegin=i;
}
else if(inExon && !exonStates.isMember(state))
{
exons.push_back(new Exon(exonBegin,i,transcriptId,
axisId,'+'));
inExon=false;
if(intergenicStates.isMember(state)) inIntergenic=true;
++exonsPerGene[transcriptId];
}
else if(!inIntergenic && intergenicStates.isMember(state))
inIntergenic=true;
else if(inIntergenic && !intergenicStates.isMember(state))
inIntergenic=false;
}
cout << "#score="<<getPathScore(path,seq,hmm)<<endl;
delete &path;
}
cout << "##gff-version 2\n"
<< "##date " << ctime(&t)
<< "##source-version homer 1.0 (Nov 2004)\n"
<< "##contact bmajoros@tigr.org\n"
<< "##type DNA\n";
produceOutput();
return 0;
}
/*
void Application::loadSubmodels(const TigrString &filename)
{
submodelOrigins.push_back(0);
int nextFreeState=1;
TigrFile file(filename);
numSubmodels=0;
while(!file.eof())
{
TigrString line=file.readLine();
if(file.eof()) break;
vector<TigrString> &fields=*line.getFields("= \t\n[]");
int numFields=fields.size();
if(numFields==1)
throw TigrString("Syntax error in submodel list file: ")+line;
if(numFields>0)
{
int modelId=fields[0].asInt();
TigrString secondField=fields[1];
TigrString modelFilename=fields[numFields-1];
HiddenMarkovModel *submodel=
new HiddenMarkovModel(modelFilename,alphabet);
while(modelId>=submodels.size()) submodels.push_back(NULL);
submodels[modelId]=submodel;
int submodelStates=submodel->countStates()-1;
++numSubmodels;
if(secondField=="exon")
addToSet(exonStates,nextFreeState,submodelStates);
else if(secondField=="intergenic")
addToSet(intergenicStates,nextFreeState,submodelStates);
submodelOrigins.push_back(nextFreeState);
nextFreeState+=submodelStates;
}
delete &fields;
}
}
*/
void Application::loadSubmodels(const TigrString &filename)
{
submodelOrigins.push_back(0);
int nextFreeState=1;
TigrFile file(filename);
numSubmodels=0;
while(!file.eof())
{
TigrString line=file.readLine();
if(file.eof()) break;
vector<TigrString> &fields=*line.getFields("= \t\n,");
int numFields=fields.size();
if(numFields==1)
throw TigrString("Syntax error in submodel list file: ")+line;
if(numFields>0)
{
TigrString type=fields[0];
TigrSet<int> *theSet=NULL;
if(type=="intergenic") theSet=&intergenicStates;
else if(type=="exon") theSet=&exonStates;
else throw TigrString("Bad type in submodels file: ")+type;
for(int i=1 ; i<numFields ; ++i)
{
int state=fields[i].asInt();
if(state>0) theSet->insert(state);
//cout<<"inserting "<<state<<" as "<<type<<endl;
}
}
delete &fields;
}
}
void Application::addToSet(TigrSet<int> &theSet,int fromState,int numStates)
{
int end=fromState+numStates;
for(int i=fromState ; i<end ; ++i)
theSet.insert(i);
}
HiddenMarkovModel *Application::loadHMM(const TigrString &filename)
{
HiddenMarkovModel *H=new HiddenMarkovModel(filename,alphabet);
return H;
}
void Exon::printOn(ostream &os)
{
os << axisId << "\thomer\t" << "exon" << "\t"
<< begin+1 << "\t" << end << "\t.\t" << strand << "\t"
<< "." <<"\ttransgrp="<< transcriptId << ";" << endl;
}
ostream &operator<<(ostream &os,Exon &exon)
{
exon.printOn(os);
return os;
}
void Application::produceOutput()
{
int n=exons.size();
for(int i=0 ; i<n ; ++i)
{
Exon *exon=exons[i];
cout << *exon;
}
}
double Application::getPathScore(vector<int> &path,Sequence &seq,
HiddenMarkovModel &hmm)
{
double logP=0;
int pathLength=path.size();
for(int i=0 ; i<pathLength ; ++i)
{
int state=path[i];
Symbol symbol=seq[i];
logP+=log(hmm.getEmissionProb(state,symbol));
if(i+1<pathLength)
logP+=log(hmm.getTransitionProb(state,path[i+1]));
}
return logP;
}