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matriz.c
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matriz.c
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#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "math.h"
#include "ctype.h"
int matrix(int *Nsus_pos)
{
/*ORDEN DE AA ALFABETICO POR NOMBRE DE AA Ala, Arg,Asn, ...*/
int orden[AA]={1,15,12,3,2,14,4,6,7,8,10,9,11,5,13,16,17,19,20,18};
FILE *outfile, *infile1;
FILE *outfile1, *outfile2;
int i,j,a,b,c;
double Nsus_sim[protsize][AA][AA];
double Qij[AA][AA];
double Qijref[AA][AA],freqref[AA];
double Qijend[AA][AA],freqend[AA],Qijref_N[AA][AA];
double Qij_rea[AA][AA];
double Pij[AA][AA];
double lambda_ref,lambda_rea,lambda,lambda_scpe;
double alpha;
double Sij[AA][AA],Sijref_N[AA][AA];
double Sijend[AA][AA];
double freq[AA],freq_rea[AA];
double sum_total,sum[AA],suma, sum_q[AA];
char filename[MAXNAME],filenamefreq[MAXNAME],filenameprob[MAXNAME];
double lambda_chico=0.000001;
double Norm(double freq[AA],double Qij[AA][AA]);
double Sum_over_j(double N[AA]);
int Print_Matrix(double N[AA][AA],FILE *out);
infile1 = fopen ("qjones.dat", "r");
sprintf(filenameprob,"%s.Prob",outmatrix_name);
sprintf(filenamefreq,"%s.Freq",outmatrix_name);
outfile2 = fopen (filenameprob, "w");
outfile1 = fopen (filenamefreq, "w");
printf("%s %s\n",filenameprob, filenamefreq);
alpha=0.01;
/*Read reference Qij */
for(i=0;i<AA;i++) {
for(j=0;j<AA;j++) fscanf(infile1,"%lf ",&Qijref[i][j]);
fscanf(infile1,"\n");
}
/*Read reference frequences*/
for(i=0;i<AA;i++) fscanf(infile1," %lf\n",&freqref[i]);
/*Make Nsus symmetric*/
for(c=0;c<protsize;c++)
for(i=0;i<AA;i++)
for(j=0;j<AA;j++) Nsus_sim[c][i][j]=0.5*(*(Nsus_pos + AA*AA*c +i*AA +j)+*(Nsus_pos + AA*AA*c +j*AA +i));
for(c=0;c<protsize;c++) {
/* Calculate Pij or Qij(i!=j)*/
sum_total=0.;
for(i=0;i<AA;i++) {
sum[i]=0.;
sum_q[i]=0.;
sum[i]=Sum_over_j(Nsus_sim[c][i]);
for(j=0;j<AA;j++) if(i!=j) {
if(sum[i]!=0) Qij[i][j]=Nsus_sim[c][i][j]/sum[i];
else Qij[i][j]=0.;
}
sum_total+=sum[i];
for(j=0;j<AA;j++) if(i!=j) sum_q[i]+=Qij[i][j];
if(sum_q[i]!=0) Qij[i][i]=-sum_q[i];
else Qij[i][i]=0.;
}
/*Calculate frecuencies*/
for(i=0;i<AA;i++) if(sum_total!=0)freq[i]= sum[i]/sum_total;
else freq[i]=0.;
/*check SumFreq=1*/
suma=0.;
for(i=0;i<AA;i++) suma+=freq[i];
if(suma!=1.) {
for(i=0;i<AA;i++) if(suma!=0) freq[i]=freq[i]/suma;
}
/*Calcular lambda Qij ref*/
lambda_ref=Norm(freqref,Qijref);
/*Calcular lambda Qij scpe*/
lambda_scpe=Norm(freq,Qij);
/*NOrmalizar Qijref con respecto a Qij scpe*/
for(i=0;i<AA;i++) for(j=0;j<AA;j++)
if(lambda_scpe!=0) Qijref_N[i][j]=(Qijref[i][j]*lambda_scpe)/lambda_ref;
else Qijref_N[i][j]=Qijref[i][j]*lambda_chico;
/*Calcular Sij_ref*/
for(i=0;i<AA;i++)
for(j=0;j<AA;j++) Sijref_N[i][j]= Qijref_N[i][j]/freqref[j];
/*Aplicar seudocuentas a Freq[c]*/
for(i=0;i<AA;i++)
freqend[i]= (freq[i] + alpha*freqref[i])/ (1.0 + alpha);
/*Calcular Sij */
for(i=0;i<AA;i++)
for(j=0;j<AA;j++) Sij[i][j]= Qij[i][j]/freqend[j];
/*Corregir Sij por seudocuentas*/
for(i=0;i<AA;i++) for(j=0;j<AA;j++)
Sijend[i][j]= (Sij[i][j] + alpha*Sijref_N[i][j])/(alpha+1.0);
/*Calculo Qijend a partir de Sijend*pj */
for(i=0;i<AA;i++) for(j=0;j<AA;j++)
Qijend[i][j]= Sijend[i][j] * freqend[j];
/*renormalizo Qijend a la velocidad de Qij (scpe)*/
lambda=0.;
lambda=Norm(freqend,Qijend);
for(i=0;i<AA;i++) for(j=0;j<AA;j++)
if(lambda!=0 || lambda_scpe!=0) Qijend[i][j]=(Qijend[i][j]*lambda_scpe)/lambda;
else Qijend[i][j]=Qijref[i][j]*lambda_chico;
/*Calculo Qijend a partir de Sijend*pj */
for(i=0;i<AA;i++) for(j=0;j<AA;j++)
Sijend[i][j]= Qijend[i][j]/freqend[j];
/*OUTPUT SECTION*/
/*Reordeno Qij Sij y Freq ya que HYPHY toma por orden alfabetico*/
for(i=0;i<AA;i++) for(j=0;j<AA;j++) Sij[orden[i]-1][orden[j]-1]=Sijend[i][j];
for(i=0;i<AA;i++) for(j=0;j<AA;j++) Qij_rea[orden[i]-1][orden[j]-1]=Qijend[i][j];
for(i=0;i<AA;i++) freq_rea[orden[i]-1]=freqend[i];
/*Make HYPHY input*/
sprintf(filename,"%s-%d.dat",outmatrix_name,c);
outfile=fopen(filename,"w");
fprintf(outfile,"/*This file contains the substitution matrix for a given position or structural class obtained with scpe*/ \n\n");
fprintf(outfile," modelType = 0;\n");
fprintf(outfile," NICETY_LEVEL = 2;\n\n\n");
fprintf(outfile," %sp%d = {20,20};\n",Options.modelname,c+1);
for(i=0;i<AA;i++)
for(j=i;j<AA;j++) {
if(i!=j){
fprintf(outfile," %sp%d[%d][%d] := a*%10.15f;\n",Options.modelname, c+1,i,j,Sij[i][j]);
fprintf(outfile," %sp%d[%d][%d] := a*%10.15f;\n",Options.modelname, c+1,j,i,Sij[j][i]);
}
}
fprintf(outfile,"\n\n");
fprintf(outfile,"freqs%s={20,1};\n",Options.modelname);
for(i=0;i<AA;i++) fprintf(outfile,"freqs%s[%d][0]=%10.8f; \n",Options.modelname,i,freq_rea[i]);
fprintf(outfile,"\n\n");
fprintf(outfile,"scpe%sp%d=0;\n",Options.modelname,c+1);
fprintf(outfile,"Model %s = (%sp%d, freqs%s,1);\n",Options.modelname,Options.modelname,c+1,Options.modelname);
fprintf(outfile,"FREQUENCY_SENSITIVE = 0;\n");
fclose(outfile);
/*Print Frecuencies*/
for(i=0;i<AA;i++) fprintf(outfile1,"%f ",freq_rea[i]);
fprintf(outfile1,"\n");
/*Print Probabilities*/
for(i=0;i<AA;i++)sum[i]=0;
for(i=0;i<AA;i++) {
for(j=0;j<AA;j++) {
if(i!=j) sum[i]+= Qij_rea[i][j];
Pij[i][j]= Qij_rea[i][j];
}
Pij[i][i]= 1. - sum[i];
}
Print_Matrix(Pij,outfile2);
}
fclose(outfile1);
fclose(outfile2);
return(0);
}
/*funciones*/
double Sum_over_j(double N[AA])
{
int i;
double sum;
sum=0.;
for(i=0;i<AA;i++) sum+=N[i];
return(sum);
}
int Print_Matrix(double N[AA][AA],FILE *out)
{
int i,j;
for(i=0;i<AA;i++) {
for(j=0;j<AA;j++) fprintf(out,"%15.15f ",N[i][j]);
fprintf(out,"\n");
}
return(0);
}
double Norm(double freq[AA],double Qij[AA][AA])
{
int i,j;
double lambda;
lambda=0.;
for(i=0;i<AA;i++) lambda+=Qij[i][i]*freq[i];
return (lambda==0. ? 0. : -lambda);
}
/*
int Calculate_freq(double *pmatrix,double *freq)
{
int i,j;
for(i=0;i<AA;++i) *(freq+i)=(*(pmatrix+(i*AA+i)));
return(0);
}*/
int Calculate_omega(double Nsus[AA][AA])
{
int i,j;
float sumN, sumS, omega,syn;
sumN=sumS=syn=0.;
for(i=0;i<AA;i++)
for(j=0;j<AA;j++) if(i!=j) sumN += Nsus[i][j];
else sumS += Nsus[i][j];
syn=(sumS - (sumN*(protsize-1)))/protsize;
printf(" sumN %f sumS %f syn %f omega %f\n",sumN,sumS,syn,sumN/(syn+sumN));
return(0);
}