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PRFCluster.cpp
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/* Updated by Zi-Ming Zhao, 07/11/2016 */
/***************************************************
* Function:
* Input Parameter:
* Output:
***************************************************/
#include "PRFCluster.h"
#ifdef __linux__
unsigned int NUM_CPU = get_nprocs_conf();
#else
unsigned int NUM_CPU = std::thread::hardware_concurrency();
#endif
PRFCluster::PRFCluster() {
flag_N_pol=0;
flag_N_div=0;
if (NUM_CPU == 0) NUM_CPU = 8;
confidence_interval=0.95;
confidence_interval=(1.0-confidence_interval)/2.0;
site_specific_flag = 0;
divtime_flag = 0;
output_format_num=0;
input_format_num=0;
species_num=0;
flag_found_pr=0;
flag_found_dr=0;
flag_found_ps=0;
flag_found_ds=0;
//Initiate parameters
pol_seqfile = "";
div_seqfile = "";
genetic_code = 1;
criterion_type = 0;
Sys_cluster=0;
MS_only=0;
ci_ma=0;
Div_time=0.0;
r_estimate=1;
ci_r=1;
ci_r_exact=0;
Nuc_replace=1;
NI_estimate=0;
modelAveraged_p_gamma=0;
}
PRFCluster::~PRFCluster() {
pol_seq.clear();
pol_seqname.clear();
div_seq.clear();
div_seqname.clear();
vec_rModels.clear();
vec_lower_r.clear();
vec_upper_r.clear();
vec_time.clear();
vec_r.clear();
vec_NI.clear();
vec_SelectedModels.clear();
vec_AllModels.clear();
vec_MA_rate.clear();
vec_lower_rate.clear();
vec_upper_rate.clear();
vec_lower_rate_ps.clear();
vec_lower_rate_pr.clear();
vec_lower_rate_ds.clear();
vec_lower_rate_dr.clear();
vec_upper_rate_ps.clear();
vec_upper_rate_pr.clear();
vec_upper_rate_ds.clear();
vec_upper_rate_dr.clear();
vec_MA_rate_ps.clear();
vec_MA_rate_pr.clear();
vec_MA_rate_ds.clear();
vec_MA_rate_dr.clear();
vec_MS_rate_ps.clear();
vec_MS_rate_pr.clear();
vec_MS_rate_ds.clear();
vec_MS_rate_dr.clear();
vec_SelectedModels_ps.clear();
vec_SelectedModels_pr.clear();
vec_SelectedModels_ds.clear();
vec_SelectedModels_dr.clear();
vec_AllModels_ps.clear();
vec_AllModels_pr.clear();
vec_AllModels_ds.clear();
vec_AllModels_dr.clear();
}
/***************************************************
* Function: Log likelihood of Bernoulli distribution. BernoulliProb= (i/n)^i*[(n-i)/n]^(n-i); prob=Log(BernoulliProb)=i*log(i/n)+(n-i)*log[(n-i)/n]
* Input Parameter:
* Output:
***************************************************/
double PRFCluster::BinomialProb(long n, long i) {
double prob = 0.0;
prob += (i==0)?0:i*log(double(i)/n);
prob += (n-i==0)?0:(n-i)*log(double(n-i)/n);
return prob;
}
/***************************************************
* Function:
* Input Parameter:
* Output:
***************************************************/
double PRFCluster::getp0pc_MK(int pos_start, int pos_end, int cs, int ce, double &p0, double &pc, int nw, int nc) {
//p0 means the whole sequence except the center part.
int non_cent_len=pos_end-pos_start-ce+cs;
if(cs==pos_start && ce==pos_end){
p0=0.0;
}else{
p0=(double)(nw-nc)/non_cent_len;
}
//pc means the center part.
int cent_len=ce-cs+1;
pc=(double)nc/cent_len;
return 1;
}
/***************************************************
* Function:
* Input Parameter:
* Output:
***************************************************/
int PRFCluster::Run(int argc, const char*argv[]) {
int i, flag=1;
////srand(1234); // to fix random number generator, to make sure the program is repeatable; need to remove for the final version of the program
try {
//Parse input parameters
if (parseParameter(argc, argv)!=1) throw 1;
if (site_specific_flag && !(Sys_cluster))
{
cout << "Can't do site_specific divergence time calculation without silent clustering -s option" <<endl;
throw 1;
}
//Check input file names
if(pol_seqfile=="" || div_seqfile=="") throw 1;
cout<<endl<<NAME<<", Version: "<<VERSION<<" ["<<LASTUPDATE<<"]"<<endl;
cout<<"Reference: "<<REFERENCE<<endl<<endl;
static time_t time_start = time(NULL);
long p_species_n=0;
//Read input seqeunces: polymorphic and divergent sequences
if (input_format_num==0){
if (readFasta(pol_seqfile, pol_seqname, pol_seq)!=1) throw "Error in reading polymorphic sequences.";
if (readFasta(div_seqfile, div_seqname, div_seq)!=1) throw "Error in reading divergent sequences.";
p_species_n=pol_seq.size();
}
else if (input_format_num==1){
if (readFastaConsensus(pol_seqfile, pol_seqname, pol_seq)!=1) throw "Error in reading polymorphic sequences.";
if (readFastaConsensus(div_seqfile, div_seqname, div_seq)!=1) throw "Error in reading divergent sequences.";
if (species_num!=0) {
p_species_n=species_num;
}
else {
cout<< "Error! The number of polymorphism sequence number has to be input when using consensus sequence!\n";
throw 1;
}
}
if (verbose==1){
//Print the sequences and their names
cout<<endl<<"Criterion used: "<<CRI(criterion_type)<<endl<<endl;
cout<<endl<<"Polymorphism data:"<<endl;
cout<<endl<<">";
for(int i=0; i<pol_seqname.size();i++){
cout<<pol_seqname[i].c_str()<<"/";
}
cout<<endl;
for(int i=0; i<pol_seq.size();i++){
cout<<pol_seq[i].c_str()<<endl;
}
cout<<endl;
cout<<endl<<"Divergence data:"<<endl;
cout<<endl<<">";
for(int i=0; i<div_seqname.size();i++){
cout<<div_seqname[i].c_str()<<"/";
}
cout<<endl;
for(int i=0; i<div_seq.size();i++){
cout<<div_seq[i].c_str()<<endl;
}
cout<<endl<<endl;
}
//Check sequences' length
for (i=0; i<pol_seq.size(); i++) {
if (div_seq[0].length()!=pol_seq[i].length()) throw "Input sequences are not equal in length.";
}
if(pol_seq[0].size()%3!=0) cout<<"Warning: the length of sequences can not be divided by 3 (codon size).\n";
//throw "Error: the length of sequences can not be divided by 3 (codon size).";
//Open and Read the lookup table for numeric integration for the specific number of species
//special attention to gamma=0,purposely put the corresponding numeric integration to 0; treat separately for this case.
if (verbose==1){
cout<<endl<<"Open and Read the lookup table for numeric integration:"<<endl;
cout<<endl<<"The number of species in the polymorphism data:"<<p_species_n<<endl;
}
int tmp_n=p_species_n; //the number of species in the polymorphism data, according to the line in the lookup table
if (p_species_n>100 and p_species_n<=1500)
{
tmp_n=98+int(p_species_n/50); //for n>100, the interval is 50 in the lookup table
}
else if (p_species_n>1500)
{
cout<<"Error! The number of sequences in the polymorphism data is over the range in the Lookup Table 1500."<<endl;
}
//cout<<"The row to be extracted in the lookup table is "<<tmp_n<<endl;
//Initialize the vectors,the size of the vector is based on the number of gamma values in the lookup table, from -50 to 50 in the interval of 0.5.
Fn1.resize(201,0.0);
Fn1_d.resize(201,0.0);
Fn2.resize(201,0.0);
Fn2_d.resize(201,0.0);
cout<<endl<<"Extract LookupTable_gx1_n_gamma_integration_50_v9.dat"<<endl;
Fn1=GammaLookupTable(tmp_n,"LookupTable_gx1_n_gamma_integration_50_v9.dat",Fn1);
cout<<endl<<"Extract LookupTable_gx1_derivative_n_gamma_50_v9.dat"<<endl;
Fn1_d=GammaLookupTable(tmp_n,"LookupTable_gx1_derivative_n_gamma_50_v9.dat",Fn1_d);
cout<<endl<<"Extract LookupTable_gx2_n_gamma_integration_50_v9.dat"<<endl;
Fn2=GammaLookupTable(tmp_n,"LookupTable_gx2_n_gamma_integration_50_v9.dat", Fn2);
cout<<endl<<"Extract LookupTable_gx2_derivative_n_gamma_50_v9.dat"<<endl;
Fn2_d=GammaLookupTable(tmp_n,"LookupTable_gx2_derivative_n_gamma_50_v9.dat",Fn2_d);
//test the sucess of assignment of values in the vectors of Fn and Fn_d
//cout<<"Test Fn1[0]: "<<Fn1[0]<<endl;
//cout<<"Test Fn1[86]: "<<Fn1[86]<<endl;
//cout<<"Test Fn1_d[0]: "<<Fn1_d[0]<<endl;
//Run the main function
RunML(pol_seq, div_seq);
//Display on screen
cout<<endl<<"Mission accomplished. (Time elapsed: ";
time_t t = time(NULL)-time_start;
int h=t/3600, m=(t%3600)/60, s=t-(t/60)*60;
if(h) cout<<h<<":"<<m<<":"<<s<<")"<<endl;
else cout<<m<<":"<<s<<")"<<endl;
}
catch (const char* e) {
cout<<e<<endl;
flag = 0;
}
catch (...) {
flag = 0;
}
return flag;
}
/***************************************************
* Function: open and read the lookup table, to extract the values for the certain species number.
* Input Parameter:the lookup table file name, p_specie_n converted tmp_n;
* Output: vector<double> Fn
***************************************************/
vector<double> PRFCluster::GammaLookupTable(int tmp_n, string input_f_name, vector<double> Fn){
double t_value; // Temporary value
string t_Fn2; // Temporary Fn
int line_n=0; // the number of the item in the file
double t_r=-199; //the Temporary gamma value
int ii=0;
ifstream myfileFn2(input_f_name.c_str());
if (!myfileFn2) throw "Error in opening GammaLookupTable...\n";
if (myfileFn2.is_open())
{
//t_r=-199;
line_n=0;
ii=0;
while ( myfileFn2.good() )
{
if (line_n>tmp_n*202 and line_n<(tmp_n+1)*202) // the number 202 is based on the number of gamma values in the lookup table, from -50 to 50 in the interval of 0.5, plus the n description column.
{
myfileFn2 >>t_value;
t_r=(ii-100.0)/2.0;
//cout<<"***r"<<t_r<<":"<<t_value<<"***\t"; // the values in the table for specific gamma
Fn[ii]=t_value;
ii+=1;
}
else
{
myfileFn2 >>t_Fn2;
}
line_n=line_n+1;
}
myfileFn2.close();
}
else
{
cout << "Unable to open file"<<endl;
}
cout <<endl<<"Vector size after extraction: "<<Fn.size()<<endl;
//cout<<"Test Fn[0]: "<<Fn[0]<<endl;
return Fn;
}
/***************************************************
* Function:
* Input Parameter:
* Output:
***************************************************/
int PRFCluster::init(long N){
vec_time.resize(N,0.0);
vec_r.resize(N,0.0);
vec_NI.resize(N,0.0);
vec_MS_rate_ps.resize(N,0.0);
vec_MS_rate_pr.resize(N,0.0);
vec_MS_rate_ds.resize(N,0.0);
vec_MS_rate_dr.resize(N,0.0);
vec_MA_rate_ps.resize(N,0.0);
vec_MA_rate_pr.resize(N,0.0);
vec_MA_rate_ds.resize(N,0.0);
vec_MA_rate_dr.resize(N,0.0);
vec_lower_rate_ps.resize(N,0.0);
vec_lower_rate_pr.resize(N,0.0);
vec_lower_rate_ds.resize(N,0.0);
vec_lower_rate_dr.resize(N,0.0);
vec_upper_rate_ps.resize(N,0.0);
vec_upper_rate_pr.resize(N,0.0);
vec_upper_rate_ds.resize(N,0.0);
vec_upper_rate_dr.resize(N,0.0);
vec_SelectedModels_ps.clear();
vec_SelectedModels_pr.clear();
vec_SelectedModels_ds.clear();
vec_SelectedModels_dr.clear();
vec_AllModels_ps.clear();
vec_AllModels_pr.clear();
vec_AllModels_ds.clear();
vec_AllModels_dr.clear();
vec_SelectedModels.clear();
vec_AllModels.clear();
vec_MA_rate.resize(N,0.0);
vec_lower_rate.resize(N,0.0);
vec_upper_rate.resize(N,0.0);
vec_rModels.clear();
vec_lower_r.resize(N,0.0);
vec_upper_r.resize(N,0.0);
return 1;
}
/***************************************************
* Function:
* Input Parameter:
* Output:
***************************************************/
int PRFCluster::output(long N){
cout<<endl<<"//Results based on model selection: "<<endl;
if(Sys_cluster==1){
cout<<endl<<"Clusters from Polymorphism Synonymous:"<<endl;
if(vec_SelectedModels_ps.size()==0){
cout<<"Note: PS=1 or 0. There is not enough information for clustering!"<<endl<<endl;
}else if(vec_SelectedModels_ps.size()==1 && vec_SelectedModels_ps[0].pos_start==vec_SelectedModels_ps[0].cs && vec_SelectedModels_ps[0].pos_end==vec_SelectedModels_ps[0].ce){
cout<<"Note: There is no cluster in this sequences for Polymorphism Synonymous"<<endl<<endl;
}else{
for(long i=0; i<vec_SelectedModels_ps.size(); i++){
//Converted the start and end positions for the cluster, the pos_start, pos_end, cs, ce according to the the option output_format_num of amino acid or nucleotide output in output()
if (output_format_num==1)
{
cout<<(vec_SelectedModels_ps[i].pos_start+1)<<" nucleotide ~ "<<(vec_SelectedModels_ps[i].pos_end+1)<<" nucleotide";
cout<<"\tcs= "<<(vec_SelectedModels_ps[i].cs+1)<<"\tce= "<<(vec_SelectedModels_ps[i].ce+1);
}
else if (output_format_num==0)
{
cout<<(vec_SelectedModels_ps[i].pos_start/3+1)<<" amino acid ~ "<<(vec_SelectedModels_ps[i].pos_end/3+1)<<" amino acid";
cout<<"\tcs= "<<(vec_SelectedModels_ps[i].cs/3+1)<<"\tce= "<<(vec_SelectedModels_ps[i].ce/3+1);
}
//cout<<vec_SelectedModels_ps[i].pos_start<<" ~ "<<vec_SelectedModels_ps[i].pos_end;
//cout<<"\tcs= "<<vec_SelectedModels_ps[i].cs<<"\tce= "<<vec_SelectedModels_ps[i].ce;
cout<<endl;
cout<<"InL0= "<<vec_SelectedModels_ps[i].InL0<<"\tInL= "<<vec_SelectedModels_ps[i].InL;
cout<<"\tAIC0= "<<vec_SelectedModels_ps[i].AIC0<<"\tAIC= "<<vec_SelectedModels_ps[i].AIC;
cout<<"\tAICc0= "<<vec_SelectedModels_ps[i].AICc0<<"\tAICc= "<<vec_SelectedModels_ps[i].AICc;
cout<<"\tBIC0= "<<vec_SelectedModels_ps[i].BIC0<<"\tBIC= "<<vec_SelectedModels_ps[i].BIC;
cout<<endl;
cout<<"P0ps= "<<vec_SelectedModels_ps[i].p0<<"\tPcps= "<<vec_SelectedModels_ps[i].pc;
cout<<endl<<endl;
}
}
}
if(Sys_cluster==1){
cout<<endl<<"Clusters from Divergence Synonymous:"<<endl;
if(vec_SelectedModels_ds.size()==0){
cout<<"Note: DS=1 or 0. There is not enough information for clustering!"<<endl<<endl;
}else if(vec_SelectedModels_ds.size()==1 && vec_SelectedModels_ds[0].pos_start==vec_SelectedModels_ds[0].cs && vec_SelectedModels_ds[0].pos_end==vec_SelectedModels_ds[0].ce){
cout<<"Note: There is no cluster in this Sequences for Divergence Synonymous"<<endl<<endl;
}else{
for(long i=0; i<vec_SelectedModels_ds.size(); i++){
//Converted the start and end positions for the cluster, the pos_start, pos_end, cs, ce according to the the option output_format_num of amino acid or nucleotide output in output()
if (output_format_num==1)
{
cout<<(vec_SelectedModels_ds[i].pos_start+1)<<" nucleotide ~ "<<(vec_SelectedModels_ds[i].pos_end+1)<<" nucleotide";
cout<<"\tcs= "<<(vec_SelectedModels_ds[i].cs+1)<<"\tce= "<<(vec_SelectedModels_ds[i].ce+1);
}
else if (output_format_num==0)
{
cout<<(vec_SelectedModels_ds[i].pos_start/3+1)<<" amino acid ~ "<<(vec_SelectedModels_ds[i].pos_end/3+1)<<" amino acid";
cout<<"\tcs= "<<(vec_SelectedModels_ds[i].cs/3+1)<<"\tce= "<<(vec_SelectedModels_ds[i].ce/3+1);
}
//cout<<vec_SelectedModels_ds[i].pos_start<<" ~ "<<vec_SelectedModels_ds[i].pos_end;
//cout<<"\tcs= "<<vec_SelectedModels_ds[i].cs<<"\tce= "<<vec_SelectedModels_ds[i].ce;
cout<<endl;
cout<<"InL0= "<<vec_SelectedModels_ds[i].InL0<<"\tInL= "<<vec_SelectedModels_ds[i].InL;
cout<<"\tAIC0= "<<vec_SelectedModels_ds[i].AIC0<<"\tAIC= "<<vec_SelectedModels_ds[i].AIC;
cout<<"\tAICc0= "<<vec_SelectedModels_ds[i].AICc0<<"\tAICc= "<<vec_SelectedModels_ds[i].AICc;
cout<<"\tBIC0= "<<vec_SelectedModels_ds[i].BIC0<<"\tBIC= "<<vec_SelectedModels_ds[i].BIC;
cout<<endl;
cout<<"P0ds= "<<vec_SelectedModels_ds[i].p0<<"\tPcds= "<<vec_SelectedModels_ds[i].pc;
cout<<endl<<endl;
}
}
}
if (site_specific_flag && vec_SelectedModels_ds.size()!=0 && vec_SelectedModels_ps.size()!=0)
{
for (long i=0;i<N;i++)
{
divergent_time[i] = divergent_time_sums[i]/divergent_time_weights[i];//model averaged divergence time for site i
}
}
else{
cout<<"Warning in site specific divergence time calculation; -ssd. There is no silent clustering for PS or DS."<<endl;
}
cout<<endl<<"Clusters from Polymorphism Replacement:"<<endl;
if(vec_SelectedModels_pr.size()==0){
cout<<"Note: PR=1 or 0. There is not enough information for clustering!"<<endl<<endl;
}else if(vec_SelectedModels_pr.size()==1 && vec_SelectedModels_pr[0].pos_start==vec_SelectedModels_pr[0].cs && vec_SelectedModels_pr[0].pos_end==vec_SelectedModels_pr[0].ce){
cout<<"Note: There is no cluster in this Sequences for Polymorphism non-Synonymous"<<endl<<endl;
}else{
for(long i=0; i<vec_SelectedModels_pr.size(); i++){
//Converted the start and end positions for the cluster, the pos_start, pos_end, cs, ce according to the the option output_format_num of amino acid or nucleotide output in output()
if (output_format_num==1)
{
cout<<(vec_SelectedModels_pr[i].pos_start+1)<<" nucleotide ~ "<<(vec_SelectedModels_pr[i].pos_end+1)<<" nucleotide";
cout<<"\tcs= "<<(vec_SelectedModels_pr[i].cs+1)<<"\tce= "<<(vec_SelectedModels_pr[i].ce+1);
}
else if (output_format_num==0)
{
cout<<(vec_SelectedModels_pr[i].pos_start/3+1)<<" amino acid ~ "<<(vec_SelectedModels_pr[i].pos_end/3+1)<<" amino acid";
cout<<"\tcs= "<<(vec_SelectedModels_pr[i].cs/3+1)<<"\tce= "<<(vec_SelectedModels_pr[i].ce/3+1);
}
//cout<<vec_SelectedModels_pr[i].pos_start<<" ~ "<<vec_SelectedModels_pr[i].pos_end;
//cout<<"\tcs= "<<vec_SelectedModels_pr[i].cs<<"\tce= "<<vec_SelectedModels_pr[i].ce;
cout<<endl;
cout<<"InL0= "<<vec_SelectedModels_pr[i].InL0<<"\tInL= "<<vec_SelectedModels_pr[i].InL;
cout<<"\tAIC0= "<<vec_SelectedModels_pr[i].AIC0<<"\tAIC= "<<vec_SelectedModels_pr[i].AIC;
cout<<"\tAICc0= "<<vec_SelectedModels_pr[i].AICc0<<"\tAICc= "<<vec_SelectedModels_pr[i].AICc;
cout<<"\tBIC0= "<<vec_SelectedModels_pr[i].BIC0<<"\tBIC= "<<vec_SelectedModels_pr[i].BIC;
cout<<endl;
cout<<"\tP0pr= "<<vec_SelectedModels_pr[i].p0<<"\tPcpr= "<<vec_SelectedModels_pr[i].pc;
cout<<endl<<endl;
}
}
cout<<endl<<"Clusters from Divergence Replacement:"<<endl;
if(vec_SelectedModels_dr.size()==0){
cout<<"Note: DR=1 or 0. There is not enough information for clustering!"<<endl<<endl;
}else if(vec_SelectedModels_dr.size()==1 && vec_SelectedModels_dr[0].pos_start==vec_SelectedModels_dr[0].cs && vec_SelectedModels_dr[0].pos_end==vec_SelectedModels_dr[0].ce){
cout<<"Note: There is no cluster in this Sequences for Divergence Replacement"<<endl<<endl;
}else{
for(long i=0; i<vec_SelectedModels_dr.size(); i++){
//Converted the start and end positions for the cluster, the pos_start, pos_end, cs, ce according to the the option output_format_num of amino acid or nucleotide output in output()
if (output_format_num==1)
{
cout<<(vec_SelectedModels_dr[i].pos_start+1)<<" nucleotide ~ "<<(vec_SelectedModels_dr[i].pos_end+1)<<" nucleotide";
cout<<"\tcs= "<<(vec_SelectedModels_dr[i].cs+1)<<"\tce= "<<(vec_SelectedModels_dr[i].ce+1);
}
else if (output_format_num==0)
{
cout<<(vec_SelectedModels_dr[i].pos_start/3+1)<<" amino acid ~ "<<(vec_SelectedModels_dr[i].pos_end/3+1)<<" amino acid";
cout<<"\tcs= "<<(vec_SelectedModels_dr[i].cs/3+1)<<"\tce= "<<(vec_SelectedModels_dr[i].ce/3+1);
}
//cout<<vec_SelectedModels_dr[i].pos_start<<" ~ "<<vec_SelectedModels_dr[i].pos_end;
//cout<<"\tcs= "<<vec_SelectedModels_dr[i].cs<<"\tce= "<<vec_SelectedModels_dr[i].ce;
cout<<endl;
cout<<"InL0= "<<vec_SelectedModels_dr[i].InL0<<"\tInL= "<<vec_SelectedModels_dr[i].InL;
cout<<"\tAIC0= "<<vec_SelectedModels_dr[i].AIC0<<"\tAIC= "<<vec_SelectedModels_dr[i].AIC;
cout<<"\tAICc0= "<<vec_SelectedModels_dr[i].AICc0<<"\tAICc= "<<vec_SelectedModels_dr[i].AICc;
cout<<"\tBIC0= "<<vec_SelectedModels_dr[i].BIC0<<"\tBIC= "<<vec_SelectedModels_dr[i].BIC;
cout<<endl;
cout<<"P0dr= "<<vec_SelectedModels_dr[i].p0<<"\tPcdr= "<<vec_SelectedModels_dr[i].pc;
cout<<endl<<endl;
}
}
if (N%3!=0) { cout<< "Warning: the length of sequence can not be divided by 3 (codon size)."<<endl;}
//Print the results of Model Averaging
if (MS_only==0) {
if (modelAveraged_p_gamma==0) {cout<<endl<<"//Results based on model averaging of gamma using different models: "<<endl;}
if (modelAveraged_p_gamma==1) {cout<<endl<<"//Results based on gamma calculated from model averaged probablity of polymorphism and divergence replacement: "<<endl;}
cout.setf(ios::left);
int width=15;
//Output the headings for the data table containing the values of gamma and other relatives.
cout.width(width); cout<<"Position\t";
if(Sys_cluster==1){
cout.width(width); cout<<"MS_PolSys\t";
cout.width(width); cout<<"MA_PolSys\t";
if(ci_ma==1){
cout.width(width); cout<<"Lower_CI_PolSys\t";
cout.width(width); cout<<"Upper_CI_PolSys\t";
}
}
cout.width(width); cout<<"MS_PolRep\t";
cout.width(width); cout<<"MA_PolRep\t";
if(ci_ma==1){
cout.width(width); cout<<"Lower_CI_PolRep\t";
cout.width(width); cout<<"Upper_CI_PolRep\t";
}
if(Sys_cluster==1){
cout.width(width); cout<<"MS_DivSys\t";
cout.width(width); cout<<"MA_DivSys\t";
if(ci_ma==1){
cout.width(width); cout<<"Lower_CI_DivSys\t";
cout.width(width); cout<<"Upper_CI_DivSys\t";
}
}
cout.width(width); cout<<"MS_DivRep\t";
cout.width(width); cout<<"MA_DivRep";
if(ci_ma==1){
cout.width(width); cout<<"\tLower_CI_DivRep\t";
cout.width(width); cout<<"Upper_CI_DivRep";
}
if(r_estimate==1){
cout.width(width); cout<<"\tDivergentTime\t";
cout.width(width); cout<<"Gamma";
if(ci_r==1){
cout.width(width); cout<<"\tLower_CI_Gamma\t";
cout.width(width); cout<<"Upper_CI_Gamma";
}
}
if(NI_estimate==1){
cout.width(width); cout<<"\tNI";
}
cout.width(width); cout<<"\tPolymorphismMutationStatus\t";
cout.width(width); cout<<"DivergenceMutationStatus";
cout<<endl;
//Output the values for the data table containing the values of gamma and other relatives.
//nucleotide/codon format output
if (output_format_num==1)
{
for(long i=0; i<N; i++) {
cout.width(width);cout<<i+1<<"\t";
//Output synonymous polymorphism model selection and model average probabilities, and confidence interval if ci_ma==1
if(Sys_cluster==1){
cout.width(width);cout<<vec_MS_rate_ps[i]<<"\t";
cout.width(width);cout<<vec_MA_rate_ps[i]<<"\t";
if(ci_ma==1){
cout.width(width);cout<<vec_lower_rate_ps[i]<<"\t";
cout.width(width);cout<<vec_upper_rate_ps[i]<<"\t";
}
}
//Output replacment polymorphism model selection and model average probabilities, and confidence interval if ci_ma==1
cout.width(width);cout<<vec_MS_rate_pr[i]<<"\t";
cout.width(width);cout<<vec_MA_rate_pr[i]<<"\t";
if(ci_ma==1){
cout.width(width);cout<<vec_lower_rate_pr[i]<<"\t";
cout.width(width);cout<<vec_upper_rate_pr[i]<<"\t";
}
//Output synonymous replacment model selection and model average probabilities, and confidence interval if ci_ma==1
if(Sys_cluster==1){
cout.width(width);cout<<vec_MS_rate_ds[i]<<"\t";
cout.width(width);cout<<vec_MA_rate_ds[i]<<"\t";
if(ci_ma==1){
cout.width(width);cout<<vec_lower_rate_ds[i]<<"\t";
cout.width(width);cout<<vec_upper_rate_ds[i]<<"\t";
}
}
//Output divergence replacement model selection and model average probabilities, and confidence interval if ci_ma==1
cout.width(width);cout<<vec_MS_rate_dr[i]<<"\t";
cout.width(width);cout<<vec_MA_rate_dr[i];
if(ci_ma==1){
cout<<"\t";cout.width(width);cout<<vec_lower_rate_dr[i]<<"\t";
cout.width(width);cout<<vec_upper_rate_dr[i];
}
//Output gamma value and confidence interval of gamma if ci_r==1
if(r_estimate==1){
cout<<"\t";cout.width(width);cout<<divergent_time[i]<<"\t";
if(vec_r[i]==50){
cout.width(width);cout<<INF;
}else if (vec_r[i]==-50){
cout.width(width);cout<<NINF;
}
else if (vec_r[i]==0 || vec_r[i]==-66){
cout.width(width);cout<<"NULL";
}
else if (vec_r[i]==-99){
cout.width(width);cout<<"NA";
}
else{
cout.width(width);cout<<vec_r[i];
}
if(ci_r==1){
if(vec_lower_r[i]==50){
cout<<"\t";cout.width(width);cout<<INF<<"\t";
}else if(vec_lower_r[i]==-50){
cout<<"\t";cout.width(width);cout<<NINF<<"\t";
}
else if(vec_lower_r[i]==0 || vec_lower_r[i]==-66){
cout<<"\t";cout.width(width);cout<<"NULL"<<"\t";
}
else if(vec_lower_r[i]==-99){
cout<<"\t";cout.width(width);cout<<"NA"<<"\t";
}
else{
cout<<"\t";cout.width(width);cout<<vec_lower_r[i]<<"\t";
}
if(vec_upper_r[i]==50){
cout.width(width);cout<<INF;
}else if(vec_upper_r[i]==-50){
cout.width(width);cout<<NINF;
}
else if(vec_upper_r[i]==0 || vec_upper_r[i]==-66){
cout.width(width);cout<<"NULL";
}
else if(vec_upper_r[i]==-99){
cout.width(width);cout<<"NA";
}
else{
cout.width(width);cout<<vec_upper_r[i];
}
}//ci_r
}//r_estimate
//Estimate Neutrality Index
if(NI_estimate==1){
if(vec_NI[i]==99){
cout<<"\t";cout.width(width);cout<<"INF";
}else if(vec_NI[i]==-99){
cout<<"\t";cout.width(width);cout<<"N-INF";
}
else if(vec_NI[i]==-66){
cout<<"\t";cout.width(width);cout<<"NULL";
}else{
cout<<"\t";cout.width(width);cout<<vec_NI[i];
}
}//NI
//Output the Replacement or Synonymous status of the mutation of polymorphism and divergence.
cout<<"\t";cout.width(width);cout<<pol_codon_consensus[i]<<"\t";
cout.width(width);cout<<div_codon_consensus[i];
cout<<endl;
}
}
//amino acid format output
else if (output_format_num==0)
{
for(long i=0; i<N/3; i++) {
cout.width(width);cout<<i+1<<"\t";
//Output synonymous polymorphism model selection and model average probabilities, and confidence interval if ci_ma==1
if(Sys_cluster==1){
cout.width(width);cout<<(vec_MS_rate_ps[i*3]+vec_MS_rate_ps[i*3+1]+vec_MS_rate_ps[i*3+2])/3<<"\t";
cout.width(width);cout<<(vec_MA_rate_ps[i*3]+vec_MA_rate_ps[i*3+1]+vec_MA_rate_ps[i*3+2])/3<<"\t";
if(ci_ma==1){
cout.width(width);cout<<(vec_lower_rate_ps[i*3]+vec_lower_rate_ps[i*3+1]+vec_lower_rate_ps[i*3+2])/3<<"\t";
cout.width(width);cout<<(vec_upper_rate_ps[i*3]+vec_upper_rate_ps[i*3+1]+vec_upper_rate_ps[i*3+2])/3<<"\t";
}
}
//Output replacment polymorphism model selection and model average probabilities, and confidence interval if ci_ma==1
cout.width(width);cout<<(vec_MS_rate_pr[i*3]+vec_MS_rate_pr[i*3+1]+vec_MS_rate_pr[i*3+2])/3<<"\t";
cout.width(width);cout<<(vec_MA_rate_pr[i*3]+vec_MA_rate_pr[i*3+1]+vec_MA_rate_pr[i*3+2])/3<<"\t";
if(ci_ma==1){
cout.width(width);cout<<(vec_lower_rate_pr[i*3]+vec_lower_rate_pr[i*3+1]+vec_lower_rate_pr[i*3+2])/3<<"\t";
cout.width(width);cout<<(vec_upper_rate_pr[i*3]+vec_upper_rate_pr[i*3+1]+vec_upper_rate_pr[i*3+2])/3<<"\t";
}
//Output synonymous replacment model selection and model average probabilities, and confidence interval if ci_ma==1
if(Sys_cluster==1){
cout.width(width);cout<<(vec_MS_rate_ds[i*3]+vec_MS_rate_ds[i*3+1]+vec_MS_rate_ds[i*3+2])/3<<"\t";
cout.width(width);cout<<(vec_MA_rate_ds[i*3]+vec_MA_rate_ds[i*3+1]+vec_MA_rate_ds[i*3+2])/3<<"\t";
if(ci_ma==1){
cout.width(width);cout<<(vec_lower_rate_ds[i*3]+vec_lower_rate_ds[i*3+1]+vec_lower_rate_ds[i*3+2])/3<<"\t";
cout.width(width);cout<<(vec_upper_rate_ds[i*3]+vec_upper_rate_ds[i*3+1]+vec_upper_rate_ds[i*3+2])/3<<"\t";
}
}
//Output divergence replacement model selection and model average probabilities, and confidence interval if ci_ma==1
cout.width(width);cout<<(vec_MS_rate_dr[i*3]+vec_MS_rate_dr[i*3+1]+vec_MS_rate_dr[i*3+2])/3<<"\t";
cout.width(width);cout<<(vec_MA_rate_dr[i*3]+vec_MA_rate_dr[i*3+1]+vec_MA_rate_dr[i*3+2])/3;
if(ci_ma==1){
cout<<"\t";cout.width(width);cout<<(vec_lower_rate_dr[i*3]+vec_lower_rate_dr[i*3+1]+vec_lower_rate_dr[i*3]+2)/3<<"\t";
cout.width(width);cout<<(vec_upper_rate_dr[i*3]+vec_upper_rate_dr[i*3+1]+vec_upper_rate_dr[i*3+2])/3;
}
//Output gamma value and confidence interval of gamma if ci_r==1
if(r_estimate==1){
cout<<"\t";cout.width(width);cout<<divergent_time[i*3]<<"\t";
if(vec_r[i*3]==50 or vec_r[i*3+1]==50 or vec_r[i*3+2]==50){
cout.width(width);cout<<"INF";
}else if (vec_r[i*3]==-50 or vec_r[i*3+1]==-50 or vec_r[i*3+2]==-50){
cout.width(width);cout<<"N-INF";
}else if (vec_r[i*3]==0 || vec_r[i*3]==-66 or vec_r[i*3+1]==0 || vec_r[i*3+1]==-66 or vec_r[i*3+2]==0 || vec_r[i*3+2]==-66 ){
cout.width(width);cout<<"NULL";
}else{
cout.width(width);cout<<(vec_r[i*3]+vec_r[i*3+1]+vec_r[i*3+2])/3;
}
if(ci_r==1){
if(vec_lower_r[i*3]==50 or vec_lower_r[i*3+1]==50 or vec_lower_r[i*3+2]==50){
cout<<"\t";cout.width(width);cout<<"INF"<<"\t";
}else if(vec_lower_r[i*3]==-50 or vec_lower_r[i*3+1]==-50 or vec_lower_r[i*3+2]==-50){
cout<<"\t";cout.width(width);cout<<"N-INF"<<"\t";
}else if(vec_lower_r[i*3]==0 || vec_lower_r[i*3]==-66 or vec_lower_r[i*3+1]==0 || vec_lower_r[i*3+1]==-66 or vec_lower_r[i*3+2]==0 || vec_lower_r[i*3+2]==-66){
cout<<"\t";cout.width(width);cout<<"NULL"<<"\t";
}else{
cout<<"\t";cout.width(width);cout<<(vec_lower_r[i*3]+vec_lower_r[i*3+1]+vec_lower_r[i*3+2])/3<<"\t";
}
if(vec_upper_r[i*3]==50 or vec_upper_r[i*3+1]==50 or vec_upper_r[i*3+2]==50){
cout.width(width);cout<<"INF";
}else if(vec_upper_r[i*3]==-50 or vec_upper_r[i*3+1]==-50 or vec_upper_r[i*3+2]==-50){
cout.width(width);cout<<"N-INF";
}else if(vec_upper_r[i*3]==0 || vec_upper_r[i*3]==-66 or vec_upper_r[i*3+1]==0 || vec_upper_r[i*3+1]==-66 or vec_upper_r[i*3+2]==0 || vec_upper_r[i*3+2]==-66){
cout.width(width);cout<<"NULL";
}else{
cout.width(width);cout<<(vec_upper_r[i*3]+vec_upper_r[i*3+1]+vec_upper_r[i*3+2])/3;
}
}//ci_r
}//r_estimate
//Estimate Neutrality Index
if(NI_estimate==1){
if(vec_NI[i*3]==99 or vec_NI[i*3+1]==99 or vec_NI[i*3+2]==99){
cout<<"\t";cout.width(width);cout<<"INF";
}else if(vec_NI[i*3]==-99 or vec_NI[i*3+1]==-99 or vec_NI[i*3+2]==-99){
cout<<"\t";cout.width(width);cout<<"N-INF";
}else if(vec_NI[i*3]==-66 or vec_NI[i*3+1]==-66 or vec_NI[i*3+2]==-66){
cout<<"\t";cout.width(width);cout<<"NULL";
}else{
cout<<"\t";cout.width(width);cout<<(vec_NI[i*3]+vec_NI[i*3+1]+vec_NI[i*3+2])/3;
}
}//NI
//Output the Replacement or Synonymous status of the mutation of polymorphism and divergence.
if (pol_codon_consensus[i*3]=='R' or pol_codon_consensus[i*3+1]=='R' or pol_codon_consensus[i*3+2]=='R') { cout<<"\tR\t"; }
else if (pol_codon_consensus[i*3]=='S' or pol_codon_consensus[i*3+1]=='S' or pol_codon_consensus[i*3+2]=='S') { cout<<"\tS\t"; }
else { cout<<"\t*\t"; }
//(pol_codon_consensus[i*3]=='*' and pol_codon_consensus[i*3+1]=='*' and pol_codon_consensus[i*3+2]=='*')
/*else { cout <<endl<<"Error in polymorphism codon consensus output, the three codon positions are not *, R or S! "<<pol_codon_consensus[i*3]<<pol_codon_consensus[i*3+1]<<pol_codon_consensus[i*3+2]<<endl;
throw 1;}
*/
if (div_codon_consensus[i*3]=='R' or div_codon_consensus[i*3+1]=='R' or div_codon_consensus[i*3+2]=='R') { cout.width(width);cout<<'R'; }
else if (div_codon_consensus[i*3]=='S' or div_codon_consensus[i*3+1]=='S' or div_codon_consensus[i*3+2]=='S') { cout.width(width);cout<<'S'; }
else { cout.width(width);cout<<'*'; }
//div_codon_consensus contains "_" in the sequence in addition to "*RS"; so program quit using else throw if not seeing *RS in output().
/*
if (div_codon_consensus[i*3]=='*' and div_codon_consensus[i*3+1]=='*' and div_codon_consensus[i*3+2]=='*') { cout.width(width);cout<<'*'; }
else { cout <<endl<<"Error in divergence codon consensus output, the three codon positions are not *, R or S! "<<div_codon_consensus[i*3]<<div_codon_consensus[i*3+1]<<div_codon_consensus[i*3+2]<<endl;
throw 1;}
*/
//cout<<"\t";cout.width(width);cout<<pol_codon_consensus[i*3]<<"\t";
//cout.width(width);cout<<div_codon_consensus[i*3];
cout<<endl;
}
}
else { throw 1;}
cout<<endl<<"Abbreviation: MS=Model Selection; MA=Model Averaging; CI=Confidence Interval; ps=Polymorphism Synonymous; pr=Polymorphism Replacement; ds=Divergence Synonymous; dr=Divergence Replacement; Gamma=N*s (Gamma: scaled selection coefficient (selection intensity); N: haploid effective population size; s: selection coefficient); NI=Neutrality Index (NI=(pr/dr)/(ps/ds), >1 Negative selection, <1 Positive selection); INF=Infinite; N-INF=Negative Infinite;"<<endl;
cout<<"NULL (Not enough information for this site or both pr=0 and dr=0); NA - gamma value is not available from our calculation."<<endl;
}
cout<<endl<<"#End of clustering"<<endl<<endl;
return 1;
}
/***************************************************
* Function:
* Input Parameter:
* Output:
***************************************************/
int PRFCluster::RunML(vector<string> pol_seq, vector<string> div_seq) {
cout<<"****** Start RunML"<<endl;
time_t time_startRunML = time(NULL); // Record the start time
long N=pol_seq[0].length();
init(N);
int q;
//if model number is not input from the user, default 10000 is used, else, use the user input Model_Number.
if (model_num_flag==0) {
Model_Number=10000;
}
pol_codon_consensus = getPolSysRep(pol_seq);
div_codon_consensus = getDivSysRep(pol_seq, div_seq);
long species_n=pol_seq.size();
if (input_format_num==1){
pol_codon_consensus = pol_seq[0];
div_codon_consensus = div_seq[0];
species_n=species_num;
}
cout<<"Polymorphism: "<<pol_codon_consensus<<endl;
cout<<"Divergence: "<<div_codon_consensus<<endl;
cout<<endl;
if(flag_N_pol==1){
cout<<endl<<"*****************"<<endl;
cout<<"Note: Nucleotide other than A, T, G or C is in the polymorphism data sequences! Please see details in manual document."<<endl;
if(Nuc_replace==1){
cout<<" It is substituted by the most frequent used nucleotide in polymorphism sequence at this site!"<<endl;
}else{
cout<<" This codon is seen as gap!"<<endl;
}
cout<<"*****************"<<endl<<endl;
}
if(flag_N_div==1){
cout<<endl<<"*****************"<<endl;
cout<<"Note: Nucleotide other than A, T, G or C is in the divergence data sequence! Please see details in manual document."<<endl;
if(Nuc_replace==1){
cout<<" It is substituted by the most frequent used nucleotide in polymorphism sequence at this site!"<<endl;
}else{
cout<<" This codon is seen as gap!"<<endl;
}
cout<<"*****************"<<endl<<endl;
}
//Print the #Div & #Pol
double ps=0.0;
double ds=0.0;
double pr=0.0;
double dr=0.0;
ps=getDifference(pol_codon_consensus,0,N-1,'S');
ds=getDifference(div_codon_consensus,0,N-1,'S');
pr=getDifference(pol_codon_consensus,0,N-1,'R');
dr=getDifference(div_codon_consensus,0,N-1,'R');
cout<<"The gene length: "<<N<<" bp"<<endl;
cout<<"PS: "<<ps<<endl;
cout<<"DS: "<<ds<<endl;
cout<<"PR: "<<pr<<endl;
cout<<"DR: "<<dr<<endl;
//Estimate the divergence time between species using the information from whole sequence.
cout<<"Number of Individuals in Polymorphism="<<species_n<<endl;
/* cout<<"Divergent Time: "<<divergent_time<<endl;
cout<<endl;
*/
cout<<"Before Clustering (Total Time elapsed: ";
time_t t2total = time(NULL)-time_startRunML;
int h=t2total/3600, m=(t2total%3600)/60, s=t2total-(t2total/60)*60;
if(h) cout<<h<<":"<<m<<":"<<s<<")"<<endl;
else cout<<m<<":"<<s<<")"<<endl;
//Use ps/pr/ds/dr information to find the cluster from the sequences
//flag_seq==0 means using pol_seq
//flag_seq==1 means using div_seq
int flag_seq=0;
//// Fixed bug due to the new OS X 10.9 system [error: variable length array of non-POD element type 'struct SiteModels']
////Solution: use a very large number instead of the parameter N for the gene length, for keeping all models for each gene site, to make sure the number is larger than the gene length.
// struct SiteModels sm_pol[N];
struct SiteModels sm_pol[10000];
struct SiteModels rep_pol[10000];
if (N>10000) { cout<<"The length of the gene exceeds 10000, Revise the SiteModels upper-boundary array size!"<<endl; throw 1;}
if(Sys_cluster==1){
//Initialize for PS
vec_SelectedModels.clear();
vec_MS_rate.clear();
vec_MA_rate.clear();
vec_lower_rate.clear();
vec_upper_rate.clear();
vec_MS_rate.resize(N,0.0);
vec_MA_rate.resize(N,0.0);
vec_lower_rate.resize(N,0.0);
vec_upper_rate.resize(N,0.0);
flag_seq=0;
cout<<"****** Start Clustering Polymorphism Sysnonymous"<<endl;
time_t time_start1 = time(NULL); // Record the start time
q = ClusterSubSeq(0, N-1,'S',flag_seq,sm_pol);
if (q == -1)
{
cout << "Error clustering (PS is too low!)" << endl;
throw 1;
}
cout<<"End Clustering Polymorphism Sysnonymous (Time elapsed: ";
time_t t2 = time(NULL)-time_start1;
h=t2/3600, m=(t2%3600)/60, s=t2-(t2/60)*60;
if(h) cout<<h<<":"<<m<<":"<<s<<")"<<endl;
else cout<<m<<":"<<s<<")"<<endl;
cout<<"End Clustering Polymorphism Sysnonymous (Total Time elapsed: ";
t2total = time(NULL)-time_startRunML;
h=t2total/3600, m=(t2total%3600)/60, s=t2total-(t2total/60)*60;
if(h) cout<<h<<":"<<m<<":"<<s<<")"<<endl;
else cout<<m<<":"<<s<<")"<<endl;
vec_SelectedModels_ps=vec_SelectedModels;
vec_MS_rate_ps=vec_MS_rate;
vec_MA_rate_ps=vec_MA_rate;
if(MS_only==0 && ci_ma==1 && ps>1){
cout<<"****** Start Model Averaging Polymorphism Sysnonymous"<<endl;
time_t time_start1 = time(NULL); // Record the start time
CI_MA(sm_pol,N);
cout<<"End Model Averaging Polymorphism Sysnonymous (Time elapsed: ";
time_t t2 = time(NULL)-time_start1;
h=t2/3600, m=(t2%3600)/60, s=t2-(t2/60)*60;
if(h) cout<<h<<":"<<m<<":"<<s<<")"<<endl;
else cout<<m<<":"<<s<<")"<<endl;
cout<<"End Model Averaging Polymorphism Sysnonymous (Total Time elapsed: ";
t2total = time(NULL)-time_startRunML;
h=t2total/3600, m=(t2total%3600)/60, s=t2total-(t2total/60)*60;
if(h) cout<<h<<":"<<m<<":"<<s<<")"<<endl;
else cout<<m<<":"<<s<<")"<<endl;
}
vec_lower_rate_ps=vec_lower_rate;
vec_upper_rate_ps=vec_upper_rate;
}
//Initialize for PR
vec_SelectedModels.clear();
vec_MS_rate.clear();
vec_MA_rate.clear();
vec_lower_rate.clear();
vec_upper_rate.clear();
vec_MS_rate.resize(N,0.0);
vec_MA_rate.resize(N,0.0);
vec_lower_rate.resize(N,0.0);
vec_upper_rate.resize(N,0.0);
flag_seq=0;
cout<<"****** Start Clustering Polymorphism Replacement"<<endl;
time_t time_start1 = time(NULL); // Record the start time
q=ClusterSubSeq(0, N-1,'R',flag_seq,rep_pol);
if (q == -1)
{
cout << "Error clustering (PR is too low!)" << endl;
throw 1;
}
cout<<"End Clustering Polymorphism Replacement (Time elapsed: ";
time_t t2 = time(NULL)-time_start1;
h=t2/3600, m=(t2%3600)/60, s=t2-(t2/60)*60;
if(h) cout<<h<<":"<<m<<":"<<s<<")"<<endl;
else cout<<m<<":"<<s<<")"<<endl;
cout<<"End Clustering Polymorphism Replacement (Total Time elapsed: ";
t2total = time(NULL)-time_startRunML;
h=t2total/3600, m=(t2total%3600)/60, s=t2total-(t2total/60)*60;
if(h) cout<<h<<":"<<m<<":"<<s<<")"<<endl;
else cout<<m<<":"<<s<<")"<<endl;
vec_SelectedModels_pr=vec_SelectedModels;
vec_MS_rate_pr=vec_MS_rate;
vec_MA_rate_pr=vec_MA_rate;