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stat.c
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stat.c
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/******************************************************************/
/* Stat.c - routine to summarise output of Interval MCMC program */
/******************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include "tools.h"
#include "ldhat.h"
long *idum;
void print_help(int argc, char *argv[]);
main(int argc, char *argv[]) {
int nline, ndat, i, j, mid, l95, u95, k, nmiss=0;
long seed = -setseed();
double **dat, av, *arr;
double drate[4];
double *locs;
int ns;
double tlseq;
char lc;
int loc_file = 0;
char fname[MAXNAME+1];
char prefix[MAXNAME+1];
FILE *ifp, *ofp;
FILE *loc=NULL;
char *in_str;
int ask_questions = 1;
print_help(argc, argv);
strcpy(prefix, "");
for(i = 0; i < argc; i++)
{
if(*argv[i] == '-')
{
ask_questions = 0;
in_str = argv[i];
if(strcmp(in_str, "-input") == 0) ifp = fopen(argv[i+1], "r");
if(strcmp(in_str, "-burn") == 0) nmiss = atoi(argv[i+1]);
if(strcmp(in_str, "-loc") == 0) {loc = fopen(argv[i+1], "r"); loc_file = 1;}
if(strcmp(in_str, "-prefix") == 0) strcpy(prefix, argv[i+1]);
}
}
if((ifp == NULL) || (ask_questions == 1))
{
printf("\nCould not find input file in command line\n");
printf("\nInput file name:");
scanf("%s", fname);
ifp = fopen(fname, "r");
}
if (!ifp) nrerror("Cannot open file");
idum = &seed;
if (loc != NULL)
{
fscanf(loc, "%i %lf %c", &ns, &tlseq, &lc);
locs = dvector(0, ns);
locs[0] = -1.0;
for (i=1; i<=ns; i++)
{
fscanf(loc, "%lf", &locs[i]);
if (i>1 && locs[i]<=locs[i-1]) nrerror("Error in locs file: SNPs must be monotonically increasing");
}
fclose(loc);
}
if (ask_questions)
{
printf("\nNumber of burn-in samples:");
scanf("%i", &nmiss);
}
if (nmiss<0) nmiss=0;
fscanf(ifp,"%i %i", &nline, &ndat);
if (nline < 2) nrerror("Too few points for analysis");
dat = dmatrix(1,nline,1,ndat);
if (nmiss>nline) nrerror("Miss more than have data points!!");
printf("\n\nReading data: %i lines (miss first %i) of %i points......",nline,nmiss,ndat);
for (i=1;i<=nline;i++) for (j=1;j<=ndat;j++) {
fscanf(ifp,"%lf", &dat[i][j]);
if (feof(ifp)) nrerror("Reached end of file unexpectedly");
}
printf("...Data read successfully\n\n");
fclose(ifp);
if ((loc_file != 0) && (ndat != ns))
{
printf("Loc file does not match input file. Ignoring\n\n");
loc_file = 0;
}
arr = dvector(1,nline-nmiss);
strcpy(fname, prefix);
ofp = fopen(strcat(fname, "res.txt"), "w");
mid = (int) ((double) (nline-nmiss)/2);
l95 = (int) ((double) (nline-nmiss)*0.025+1.0);
u95 = (int) ((double) (nline-nmiss)*0.975);
printf("\n\nMid = %i, L95=%i, U95=%i\n\n", mid, l95, u95);
fprintf(ofp,"Loci\tMean_rho\tMedian\tL95\tU95");
for (i=1;i<=ndat;i++) {
printf("."); if (!i%50) printf("\n");
for (j=1+nmiss,av=0;j<=nline;j++) {
av+=dat[j][i];
arr[j-nmiss]=dat[j][i];
}
av/=(double) (nline-nmiss);
/* printf("Initial array: "); for (k=1;k<=nline-nmiss;k++) printf(" %8.5f",arr[k-nmiss]);*/
sort_farray(arr,nline-nmiss);
/* printf("\nSorted array: "); for (k=1;k<=nline-nmiss;k++) printf(" %8.5f",arr[k-nmiss]);
printf("\n\n");
*/
if (loc_file == 0)
fprintf(ofp,"\n%6i\t%10.5f\t%10.5f\t%10.5f\t%10.5f",i-1,av,arr[mid],arr[l95],arr[u95]);
else
fprintf(ofp,"\n%10.3f\t%10.5f\t%10.5f\t%10.5f\t%10.5f",locs[i-1],av,arr[mid],arr[l95],arr[u95]);
}
/*Count total rate jumped over region*/
for (i=1+nmiss, drate[0]=drate[2]=0.0;i<=nline;i++) {
for (j=2,drate[1]=drate[3]=0.0;j<ndat-1;j++) {
drate[1]+=(double) fabs(dat[i][j+1]-dat[i][j]);
if (dat[i][j+1]!=dat[i][j]) drate[3]++;
}
drate[0]+=drate[1];
drate[2]+=drate[3];
}
drate[0]/=(double) nline-nmiss;
drate[2]/=(double) nline-nmiss;
printf("\n\nAverage total change in rate = %.3f\nAverage total # changes = %.3f\n\n", drate[0],drate[2]);
if (loc_file != 0)
free_dvector(locs, 0, ns);
fclose(ofp);
}
sort_farray(double *arr, int n) {
int pass, i;
double tmp;
for (pass=1;pass<=n;pass++) for (i=1;i<n;i++) {
if (arr[i+1]<arr[i]) {
tmp=arr[i+1];
arr[i+1]=arr[i];
arr[i]=tmp;
}
}
}
void print_help(int argc, char* argv[])
{
int i;
char *in_str;
for(i = 0; i < argc; i++){
if(*argv[i] == '-'){
in_str = argv[i];
if((strcmp(in_str, "-h") == 0) || (strcmp(in_str, "-?") == 0) || (strcmp(in_str, "-help") == 0)) {
printf("\nstat\n");
printf("Summarise output from interval\n\n");
printf("Required Options :\n");
printf("-input <file> Input file (rates.txt or bounds.txt)\n");
printf("\n\n");
printf("Additional Options :\n");
printf("-burn <int> Number of burn-in samples (default 0)\n");
printf("-loc <file> SNP loci file\n");
printf("-prefix <string> Prefix of output files\n");
printf("\n\n");
exit (0);
}
}
}
}