YuuMJ1997/EukPhylo
1
0
Fork 0
mirror of http://43.156.76.180:8026/YuuMJ/EukPhylo.git synced 2025-12-28 07:10:24 +08:00
Code Issues Packages Projects Releases Wiki Activity
EukPhylo/PTL2/Scripts-GRID/guidance.v2.02/libs/phylogeny/codon.cpp
Katzlab dd76ab1d12 Added PTL2 Scripts 
These are PTL2 files from Auden 2/9
2023-02-14 11:20:52 -05:00

561 lines
15 KiB
C++
Raw Blame History

// $Id: codon.cpp 5981 2009-03-17 14:39:39Z rubi $
#include "codon.h"
#include "nucleotide.h"
#include "amino.h"
#include "logFile.h"
#include "definitions.h"
#include "someUtil.h"
#include "matrixUtils.h"
#include "sequenceContainer.h"
#include <sstream>
#include <cctype>
#define INITIATION_CODON "i"
vector<vector<codonUtility::diffType> > codonUtility::_trtvDiff;
vector<vector<codonUtility::replacementType> > codonUtility::_synNonsynDiff;
vector<vector<codonUtility::nucDiffPlaceType> > codonUtility::_nucDiffPlace;
vector<vector<codonUtility::nucsDiffType> > codonUtility::_nucsDiff;
codon::codon(){
geneticCodeString gcs=geneticCodeHolder::nuclearStandard;
init(gcs);
}
codon::codon(const geneticCodeString& matrixFileString){
init(matrixFileString);
}
void codon::init(const geneticCodeString& matrixFileString)
{
readMatrixFromFile(matrixFileString.Val);
}
void codon::readMatrixFromFile(const string& matrixFileName){ //default value: "nuclearCode.txt"
// cout<<"in codon constructor"<<endl;
stringstream in(matrixFileName.c_str());
if (!in) {
errorMsg::reportError("in codon::readMatrixFromFile: unable to open matrix data file");
}
int aa = -1; //initialized as -1 so in first iteration will change to 0
int noOfCodons = 0;
string strAmino;
bool isInitCodon = false;
while (!in.eof()) { //20 amino acids and stop
string val;
in>>val;
if (val.size()==1) { //amino acid
if(val == INITIATION_CODON)
isInitCodon = true;
else{
aa++;
strAmino=val;
if (strAmino=="*") { _alphabetSize=noOfCodons;}
isInitCodon = false;
}
}
else if (val.size()==3 && val[0]!='#'){ //codon, # symbolizes a comment
if(isInitCodon){
map <string,int>::const_iterator iniItr =_codon2Int.find(val);
if(iniItr == _codon2Int.end())
errorMsg::reportError("Initiation codon with undefined index at codon::readMatrixFromFile");
else
_initiationIndex2codon[iniItr->second] = val;
}
else{
_geneticCode[val]=strAmino;
_codon2Int[val]=noOfCodons;
noOfCodons++;
}
}
else {
if (noOfCodons!=64){
string err="in codon::readMatrixFromFile: total number of codons = "+int2string(noOfCodons);
errorMsg::reportError(err);
}
return;
}
}
}
codon& codon::operator=(const codon& other) {
_geneticCode = other._geneticCode; //key - codon, value - amino acid
_codon2Int = other._codon2Int;//key string of codon int= integer value of codon
_alphabetSize = other._alphabetSize;
_initiationIndex2codon = other._initiationIndex2codon;
return *this;
}
// codon::codon(const codon& other):
// _geneticCode(other._geneticCode), //key - codon, value - amino acid
// _codon2Int(other._codon2Int),//key string of codon int= integer value of codon
// _alphabetSize(other._alphabetSize){}
//return -99 if not succeeds.
int codon::fromChar(const string& s, const int pos) const {
if (s.size() <= pos+2) {
//errorMsg::reportError("Trying to read a codon pass the end of the string. The number of nucleotide may not be divisible by three");
string textToPrint("Trying to read a codon pass the end of the string. The number of nucleotide may not be divisible by three");
LOG(1,<<textToPrint<<endl);
return -99;
}
nucleotide nuc;
int p1,p2,p3;
p1 = nuc.fromChar(s[pos]);
p2 = nuc.fromChar(s[pos+1]);
p3 = nuc.fromChar(s[pos+2]);
if ((p1 <0) || (p2 <0) || (p3 <0))
return gap();
else if ((p1 ==15) || (p2 ==15) || (p3 ==15)) return unknown(); // unknown.
else if ((p1 >4) || (p2 >4) || (p3 >4)) return unknown(); //unknown.
string strCodon="";
//change U --> T
if (p1==4) strCodon+="T";
else strCodon+=toupper(s[pos]);
if (p2==4) strCodon+="T";
else strCodon+=toupper(s[pos+1]);
if (p3==4) strCodon+="T";
else strCodon+=toupper(s[pos+2]);
//const string strCodon = s.substr(pos,3);
map <string,int> tmpMap=_codon2Int;
map <string,int>::iterator it1;
it1=tmpMap.find(strCodon);
if (it1==tmpMap.end()){
string err="error in codon::fromChar cannot find codon "+strCodon;
errorMsg::reportError(err);
}
return tmpMap[strCodon];
}
vector<int> codon::fromString(const string &str) const {
vector<int> vec;
if (str.size()%3!=0) {
errorMsg::reportError("error in function codon::fromString. String length should be a multiplication of 3");
}
for (int i=0;i<str.size();i+=3)
vec.push_back(fromChar(str,i));
return vec;
}
string codon::fromInt(const int in_id) const{
if (in_id == unknown())
return "XXX";
if (in_id == gap())
return "---";
map <string, int> tmpMap = _codon2Int;
map <string, int>::iterator it=tmpMap.begin();
while (it!=tmpMap.end()){
if ((*it).second==in_id){
return (*it).first;
}
it++;
}
string err="error in function codon::fromInt: no codon found for the integer";
errorMsg::reportError(err);
return (string("we should never get here - the reportError above will exit"));
}
codonUtility::replacementType codonUtility::codonReplacement(const int c1, const int c2, const codon &cod){
if (c1 == c2) return codonUtility::sameCodon;
else if (codonUtility::aaOf(c1,cod) == codonUtility::aaOf(c2,cod)) return codonUtility::synonymous;
return codonUtility::non_synonymous;
}
int codonUtility::aaOf(const int c1, const codon &cod){
amino a;
if (c1==cod.gap())
return a.gap();
if (c1==cod.unknown())
return a.unknown();
string strCodon=cod.fromInt(c1);
map <string,string> geneticCode=cod.geneticCode();
map <string,string>::iterator pos;
if ((pos=geneticCode.find(strCodon)) == geneticCode.end()){
string err="error in codonUtility::aaOf: cannot find codon "+strCodon;
errorMsg::reportError(err);
}
if (pos->second.size() > 1){
errorMsg::reportError("error in codonUtility::aaOf: amino acid 1 letter code > 1");
}
return a.fromChar(*pos->second.c_str());
}
codonUtility::diffType codonUtility::codonDiff(const int c1, const int c2, const codon &cod){
if (c1==c2) return codonUtility::equal;
nucleotide n;
string s1 = cod.fromInt(c1);
string s2 = cod.fromInt(c2);
int pos1 = n.fromChar(s1[0])+n.fromChar(s2[0]);
int pos2 = n.fromChar(s1[1])+n.fromChar(s2[1]);
int pos3 = n.fromChar(s1[2])+n.fromChar(s2[2]);
if (s1[0]!=s2[0] && s1[1]!=s2[1] && s1[2]!=s2[2])
return codonUtility::threesub;
if (s1[0]==s2[0] && s1[1]==s2[1] && s1[2]!=s2[2]) {
if (pos3%2==0) return codonUtility::tr;
else return codonUtility::tv;
}
if (s1[1]==s2[1] && s1[2]==s2[2] && s1[0]!=s2[0]) {
if (pos1%2==0) return codonUtility::tr;
else return codonUtility::tv;
}
if (s1[0]==s2[0] && s1[2]==s2[2] && s1[1]!=s2[1]) {
if (pos2%2==0) return codonUtility::tr;
else return codonUtility::tv;
}
if (s1[0]==s2[0] && pos2%2==0 && pos3%2==0)
return codonUtility::twoTrs;
if (s1[1]==s2[1] && pos1%2==0 && pos3%2==0)
return codonUtility::twoTrs;
if (s1[2]==s2[2] && pos1%2==0 && pos2%2==0)
return codonUtility::twoTrs;
if (s1[0]==s2[0] && pos2%2!=0 && pos3%2!=0)
return codonUtility::twoTvs;
if (s1[1]==s2[1] && pos1%2!=0 && pos3%2!=0)
return codonUtility::twoTvs;
if (s1[2]==s2[2] && pos1%2!=0 && pos2%2!=0)
return codonUtility::twoTvs;
return codonUtility::trtv;
}
//return the place (0, 1, or 2) that the two codons are different
//and the identity of the different nucleotide in the target codon.
//For example, nucDiffPlace(ATG, ACG) retruns C2
codonUtility::nucDiffPlaceType codonUtility::nucDiffPlace(const int fromCodon, const int targetCodon, const codon &cod){
if (fromCodon == targetCodon)
return codonUtility::EQUAL;
codonUtility::nucDiffPlaceType res = A1;
nucleotide nuc;
string s1 = cod.fromInt(fromCodon);
string s2 = cod.fromInt(targetCodon);
int diffNum = 0;
if (s1[0] != s2[0]){
++diffNum;
switch (s2[0])
{
case 'A': res = A1;
break;
case 'C': res = C1;
break;
case 'G': res = G1;
break;
case 'T': res = T1;
break;
default:
errorMsg::reportError("error in codonUtility::nucDiffPlace.");
break;
}
}
if (s1[1] != s2[1]){
++diffNum;
switch (s2[1])
{
case 'A': res = A2;
break;
case 'C': res = C2;
break;
case 'G': res = G2;
break;
case 'T': res = T2;
break;
default:
errorMsg::reportError("error in codonUtility::nucDiffPlace.");
break;
}
}
if (s1[2] != s2[2]){
++diffNum;
switch (s2[2])
{
case 'A': res = A3;
break;
case 'C': res = C3;
break;
case 'G': res = G3;
break;
case 'T': res = T3;
break;
default:
errorMsg::reportError("error in codonUtility::nucDiffPlace.");
break;
}
}
if (diffNum == 0)
errorMsg::reportError("error in codonUtility::nucDiffPlace. Can't find different nucleotide");
if (diffNum > 1)
res = MUL_SUB;
return res;
}
//return the different nucleotides between the fron and target codons.
//For example, nucsPlace(ATG, ACG) retruns TC
codonUtility::nucsDiffType codonUtility::nucsDiff(const int fromCodon, const int targetCodon, const codon &cod){
if (fromCodon == targetCodon)
return codonUtility::SAME;
codonUtility::nucsDiffType res = AC;
nucleotide nuc;
string s1 = cod.fromInt(fromCodon);
string s2 = cod.fromInt(targetCodon);
int diffNum = 0;
int from = 0;
int to = 0;
if (s1[0] != s2[0])
{
++diffNum;
from = s1[0];
to = s2[0];
}
if (s1[1] != s2[1])
{
++diffNum;
from = s1[1];
to = s2[1];
}
if (s1[2] != s2[2])
{
++diffNum;
from = s1[2];
to = s2[2];
}
switch(from)
{
case 'A':
switch(to)
{
case 'G':res = AG;break;
case 'T':res = AT;break;
case 'C':res = AC;break;
default:
errorMsg::reportError("error in codonUtility::nucsDiff.");
break;
}
break;
case 'G':
switch(to)
{
case 'A':res = AG;break;
case 'T':res = GT;break;
case 'C':res = CG;break;
default:
errorMsg::reportError("error in codonUtility::nucsDiff.");
break;
}
break;
case 'C':
switch(to)
{
case 'G':res = CG;break;
case 'T':res = CT;break;
case 'A':res = AC;break;
default:
errorMsg::reportError("error in codonUtility::nucsDiff.");
break;
}
break;
case 'T':
switch(to)
{
case 'G':res = GT;break;
case 'A':res = AT;break;
case 'C':res = CT;break;
default:
errorMsg::reportError("error in codonUtility::nucsDiff.");
break;
}
break;
default:
errorMsg::reportError("error in codonUtility::nucsDiff.");
break;
}
if (diffNum == 0)
errorMsg::reportError("error in codonUtility::nucsDiff. Can't find different nucleotide");
if (diffNum > 1)
res = DIFF;
return res;
}
void codonUtility::initSubMatrices(const codon& cod){
if ((_trtvDiff.size() == cod.size()) && (_synNonsynDiff.size() == cod.size()) && (_nucDiffPlace.size() == cod.size()) && (_nucsDiff.size() == cod.size()))
return;
_trtvDiff.resize(cod.size());
_synNonsynDiff.resize(cod.size());
_nucDiffPlace.resize(cod.size());
_nucsDiff.resize(cod.size());
for (int i = 0; i < _trtvDiff.size(); ++i)
{
_trtvDiff[i].resize(cod.size());
_synNonsynDiff[i].resize(cod.size());
_nucDiffPlace[i].resize(cod.size());
_nucsDiff[i].resize(cod.size());
}
//resizeMatrix<diffType>(_trtvDiff, cod.size(), cod.size());
//resizeMatrix<replacementType>(_synNonsynDiff, cod.size(), cod.size());
//resizeMatrix<nucDiffPlaceType>(_nucDiffPlace, cod.size(), cod.size());
for (int i = 0; i < cod.size(); ++i){
for (int j =0; j <= i; ++j){
_trtvDiff[i][j] = _trtvDiff[j][i] = codonDiff(i, j, cod);
_synNonsynDiff[i][j] = _synNonsynDiff[j][i] = codonReplacement(i, j, cod);
_nucDiffPlace[i][j] = nucDiffPlace(i, j, cod);
_nucDiffPlace[j][i] = nucDiffPlace(j, i, cod);
_nucsDiff[i][j] = nucsDiff(i,j,cod);
_nucsDiff[j][i] = nucsDiff(j,i,cod);
}
}
}
//returns the number (codonCounter) and frequency (codonUsage) of each codon in the sequnece container
void codonUtility::getCodonUsage(const sequenceContainer& sc, Vint& codonCounter, Vdouble& codonUsage)
{
if (sc.getAlphabet()->size() != 61)
errorMsg::reportError("cannot calculate codon usage when alphabet is not codon");
codonCounter.resize(61, 0);
codonUsage.resize(61, 0.0);
codon alph;
int sum = 0;
for (int s = 0; s < sc.numberOfSeqs();++s) {
int id = sc.placeToId(s);
for (int pos = 0; pos < sc.seqLen(); ++pos)
{
int cod = sc[id][pos];
if (alph.isSpecific(cod))
{
++sum;
++codonCounter[cod];
}
}
}
for (int c = 0; c < codonCounter.size(); ++c)
codonUsage[c] = static_cast<MDOUBLE>(codonCounter[c]) / sum;
}
//in codonUsageFile: only 3-letter-codon and frequency seperated by "\t"
void codonUtility::readCodonUsage(const string& codonUsageFileName, Vdouble& codonUsage,const codon &alph)
{
codonUsage.resize(alph.size(), 0.0);
ifstream inFile(codonUsageFileName.c_str());
vector<string> inFileData;
putFileIntoVectorStringArray(inFile, inFileData);
inFile.close();
if (inFileData.empty()){
errorMsg::reportError("unable to open file, or file is empty in codonUtility::readCodonUsage");
}
vector<string>::const_iterator it = inFileData.begin();
for (; it!= inFileData.end(); ++it)
{
if (it->empty()) //empty line
continue;
int endCodon = it->find_first_of("\t", 0);
int startFreq = it->find_first_not_of("\t ", endCodon);
if (startFreq>0)
{
string codonStr = it->substr(0, endCodon);
string freqStr = it->substr(startFreq);
MDOUBLE freq = string2double(freqStr);
if(freq == 0.0) freq = EPSILON;
codonUsage[alph.fromChar(codonStr, 0)] = freq;
}
}
}
//calculates the CAI for the whole MSA and for each position.
//The calculation is based on a pre-calculated codonUsage vector.
//The calculation is based on Sharp & Li (1987) NAR, 15:1281-1295
MDOUBLE codonUtility::calcCodonAdaptationIndex(const sequenceContainer& sc, const Vdouble& codonUsage, Vdouble& cai4site)
{
//the returned value: calculated as the average CAI for the MSA, rather than the geometrical mean as in Sharp & Li
MDOUBLE wholeAlignmentCai = 0.0;
codon alph;
amino am;
//1. calculate Wk = the frequency of codon k relative to the frequency of the optimal codon for that amino acid.
Vdouble Wk(codonUsage.size(), 0.0);
int aaId;
for (aaId = 0; aaId < am.size(); ++aaId)
{
Vint codonsOfAa = aminoUtility::codonOf(aaId, alph);
//finding the most frequent codon for this aa
MDOUBLE mostFrequent = 0.0;
Vint::const_iterator iter;
for (iter = codonsOfAa.begin(); iter != codonsOfAa.end(); ++iter)
{
if (codonUsage[*iter] > mostFrequent)
mostFrequent = codonUsage[*iter];
}
//calculating Wk
for (iter = codonsOfAa.begin(); iter != codonsOfAa.end(); ++iter)
Wk[*iter] = codonUsage[*iter] / mostFrequent;
}
//2. calculate CAI
cai4site.resize(sc.seqLen(), 0.0);
int pos;
for (pos = 0; pos < sc.seqLen(); ++pos)
{
MDOUBLE cai = 0.0;
int informativeCodons = 0;
for (int s = 0; s < sc.numberOfSeqs();++s)
{
int id = sc.placeToId(s);
int cod = sc[id][pos];
if(!alph.isSpecific(cod))
continue;
cai += Wk[cod];
++informativeCodons;
}
cai /= static_cast<MDOUBLE>(informativeCodons);
cai4site[pos] = cai;
wholeAlignmentCai += cai;
}
return wholeAlignmentCai;
}
bool codon::isStopCodon(const int in_id) const
{
if (in_id == unknown()) return false;
if (in_id == gap()) return false;
if ((in_id >= 0 ) && (in_id < _alphabetSize)) return false;
return true;
}
bool codon::isInitiationCodon(const int in_id) const
{
bool result = true;
map <int,string>::const_iterator itr = _initiationIndex2codon.find(in_id);
if(itr == _initiationIndex2codon.end()){
result = false;
}
return result;
}
Reference in New Issue View Git Blame Copy Permalink