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niceStats.c
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niceStats.c
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/******* niceStats.c ********
for calculating sample stats from MS output
********************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "msGeneralStats.h"
#define LINEBUF 1000000
void usage();
int maxsites = 100000 ;
int main(argc,argv)
int argc;
char *argv[];
{
int nsam, i, howmany ,nwins, siteIdx;
char **list, **cmatrix(), line[LINEBUF+1] ;
FILE *fopen(), *pfin ;
double *posit ;
int segsites, count , nadv, iss, h, exponent1, exponent2;
double pi , th, z, H, mfda, tajD,w, wins[50],max, min, temp_site, thetaA, thetaHPi, tajDX, achazD, h1, h2, h12, thetaW;
double winsH1[50], winsH2[50], winsH12[50];
char dum[50], astr[100] ;
double *harmonicSums;
double ehh, rehh;
int *haplotype_counts;
/* read in first two lines of output (parameters and seed) */
pfin = stdin ;
fgets( line, LINEBUF, pfin);
sscanf(line," %s %d %d", dum, &nsam, &howmany);
fgets( line, LINEBUF, pfin);
if( argc > 1 ) {
nadv = atoi( argv[1] ) ;
}
list = cmatrix(nsam,maxsites+1);
posit = (double *)malloc( maxsites*sizeof( double ) ) ;
count=0;
//print header
nwins=5;
//printf("pi\tss\tthetaH\ttajD\tfayWuH\tHapCount");
//output used for soft shoulder analysis:
//printf("pi\tss\tthetaH\ttajD\tfayWuH\tHapCount\tH1\tomegaCenter\tZnS");
//output used for spatial svm:
printf("pi\tss\tthetaH\ttajD\tfayWuH\tmaxFDA\tHapCount\tH1\tH12\tH2/H1\tOmega\tZnS");
/*for (exponent1 = -20; exponent1 <= 20; exponent1++){
for (exponent2 = -20; exponent2 < exponent1; exponent2++) {
printf("\tachazsD_%d_%d", exponent1,exponent2);
}
}*/
/*for (exponent1 = -50; exponent1 <= 50; exponent1++){
printf("\tthetaA_%d", exponent1);
}*/
//for(i=0;i<nwins;i++)printf("\tH12_win%d\tH2/H1_win%d",i,i);
printf("\n");
while( howmany-count++ ) {
/* read in a sample */
do {
fgets( line, LINEBUF, pfin);
}while ( line[0] != '/' );
fscanf(pfin," segsites: %d", &segsites );
if( segsites >= maxsites){
maxsites = segsites + 10 ;
posit = (double *)realloc( posit, maxsites*sizeof( double) ) ;
biggerlist(nsam,maxsites, list) ;
}
if( segsites > 0) {
fscanf(pfin," %s", astr);
for( i=0; i<segsites ; i++) fscanf(pfin," %lf",posit+i) ;
for( i=0; i<nsam;i++) fscanf(pfin," %s", list[i] );
}
/* analyse sample ( do stuff with segsites and list) */
haplotype_counts = (int *)malloc( nsam*sizeof( int ) ) ;
iss = segSites(segsites,nsam,list);
pi = nucdiv(nsam, segsites, list) ;
mfda = maxFDA(nsam, segsites, list);
th = thetah(nsam, segsites, list) ;
h = nHaplotypes(segsites,nsam,list);
getHaplotypeFreqSpec(segsites, nsam, list, haplotype_counts);
h1 = petrovH1(haplotype_counts,nsam);
h2 = petrovH2(haplotype_counts,nsam);
h12 = petrovH12(haplotype_counts,nsam);
H = th-pi;
tajD = tajd(nsam,segsites,pi);
//ehh = meanEHH(segsites, posit, 0.25, nsam, list);
//rehh = meanREHH(segsites, posit, 0.25, nsam, list);
//thetaHPi = achazThetaHPi(nsam, segsites, list);
//thetaW = achazThetaExponentWeights(nsam,segsites,list,-1);
//tajDX = achazTajimasDExtreme(nsam, segsites, list);
z = ZnS( segsites, nsam, list);
/*OmegaCenter*/
//Get snp that is nearest to our fixation but on the right (omegaCenter treats this focal SNP as being in the right window)
/*
min = (fabs(0.5 - posit[0]));
siteIdx = segsites-1;
for (i = 0; i < segsites; ++i){
temp_site = posit[i];
if (temp_site >= 0.5 && fabs(0.5 - temp_site) <= min){
siteIdx = i;
min = fabs(0.5-temp_site);
}
}
w = omegaCenter(siteIdx, segsites, nsam, list);
*/
w = omegaMax(segsites, nsam,list);
//printf("%lf\t%d\t%lf\t%lf\t%lf\t%d\t%f\t%f", pi, iss, th ,tajD,H, h, z, w);
//output used for soft shoulders manuscript:
//printf("%lf\t%d\t%lf\t%lf\t%lf\t%d\t%f\t%f\t%f", pi, iss, th ,tajD,H, h, h1, w, z);
//output used for spatial SVM
printf("%lf\t%d\t%lf\t%lf\t%lf\t%lf\t%d\t%d\t%lf\t%lf\t%lf\t%lf\t%lf", pi, iss, th, tajD, H, mfda, h, h1, h12, h2/h1, w, z);
//printf("%lf\t%d\t%lf\t%lf\t%lf\t%d", pi, iss, th ,tajD,H, h);
/*for (exponent1 = -50; exponent1 <= 50; exponent1++){
thetaA = achazThetaExponentWeights(nsam,segsites,list,exponent1);
printf("\t%f", thetaA);
}*/
/*harmonicSums = compute_HarmonicSums(nsam);
for (exponent1 = -20; exponent1 <= 20; exponent1++){
for (exponent2 = -20; exponent2 < exponent1; exponent2++) {
achazD = achazNeutTestExponentWeights(nsam,segsites,list,exponent1,exponent2,harmonicSums);
printf("\t%f", achazD);
}
}*/
//window stats
//tajdWindow( nwins, posit, wins, nsam, segsites,list);
//petrovHStatsWindow(segsites, nwins, posit, winsH12, winsH1, winsH2, nsam, list);
/*
//get max for normalizing windows
max=0.0;
for( i=0; i<nwins ; i++){
if (wins[i] > max){
max = wins[i];
}
}
//print windows
for( i=0; i<nwins ; i++){
if (max == 0.0){ // Prevent "-nans" in output.
printf("\t%f", 0.0);
}
else{
printf("\t%f\t%f",winsH12[i],winsH2[i]/winsH1[i]);
//printf("\t%f",wins[i]/max);
}
}*/
//free(harmonicSums);
free(haplotype_counts);
printf("\n");
}
return(0);
}