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GeneDropping.c
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GeneDropping.c
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#include <stdio.h>
#include <stdlib.h>
#include <time.h>
#include <math.h>
#include "MersenneTwister.h"
MTRand twist;
// integer from 0 to n-1
int randInt(int max) {
//return (int)((float) max*rand()/(RAND_MAX+1.0));
return twist.randInt(max-1);
}
// float in range
float randRange(int a, float b) {
//return ( (b-a) * ((float) rand() / (RAND_MAX+1.0)) )+a;
return twist.rand(b-a) + a;
}
// do the Allele selection
int randAllele(int numMom, int numDad, float selection) {
if ((numMom == 0) && (numDad == 0)) {
return 0;
}
else if ((numMom == 1) && (numDad == 0)) {
return randInt(2);
}
else if ((numMom == 2) && (numDad == 0)) {
return 1;
}
else if ((numMom == 0) && (numDad == 1)) {
return randInt(2);
}
else if ((numMom == 1) && (numDad == 1)) {
float val = randRange(0,(3+selection));
if (val < 1.0) {
return 0;
}
else if (val < 3.0) {
return 1;
}
else {
return 2;
}
}
else if ((numMom == 2) && (numDad == 1)) {
float val = randRange(0,(1+selection));
if (val < 1.0) {
return 1;
}
else {
return 2;
}
}
else if ((numMom == 0) && (numDad == 2)) {
return 1;
}
else if ((numMom == 1) && (numDad == 2)) {
float val = randRange(0,(1+selection));
if (val < 1.0) {
return 1;
}
else {
return 2;
}
}
else if ((numMom == 2) && (numDad == 2)) {
return 2;
}
}
struct genocount {
int AA, Aa, aa;
};
void init_genocount (struct genocount* thisinstance) {
thisinstance->AA = 0;
thisinstance->Aa = 0;
thisinstance->aa = 0;
}
int main(int argc, char** argv) {
// test for correct inputs
if (argc != 2) {
printf("Usage: ./GeneDropping [config file]\n\n");
printf("Config file format (one per line): \n 1) path/name of pedigree file\n 2) number of hutterites in pedigree\n 3) number of founders in pedigree\n 4) path/name of cohort file\n 5) number of cohorts in the file (assumes that 0 counts as a group containing all no-cohort findivs)\n 6) number of sims desired per founder\n 7) fitness penalty of mutations (0 to 1)\n 8) path/name of output file\n\n");
exit(1);
}
// load information from config file
int numHut, numFounder, num_cohorts, num_desired, selection;
// char *pedfile; // initialize pointers to files
// char *cohortfile; // initialize pointers to files
// char *outputfile; // initialize pointers to files
char pedfile[2000];
char cohortfile[2000];
char outputfile[2000];
// printf("Loading information from config file\n"); // DEBUG
FILE* configfile = fopen(argv[1], "r");
if (configfile == NULL) {
printf("ERROR: Config file does not exist\n");
exit(1);
}
fscanf(configfile, "%s", pedfile);
printf("Pedigree file = %s\n", pedfile); // DEBUG
fscanf(configfile, "%i", &numHut);
printf("Number of Hutterites in pedigree = %i\n", numHut); // DEBUG
fscanf(configfile, "%i", &numFounder);
printf("Number of founders in pedigree = %i\n", numFounder); // DEBUG
fscanf(configfile, "%s", cohortfile);
printf("Cohort file = %s\n", cohortfile); // DEBUG
fscanf(configfile, "%i", &num_cohorts);
printf("Number of cohorts = %i\n", num_cohorts); // DEBUG
fscanf(configfile, "%i", &num_desired);
printf("Number of simulations per founder = %i\n", num_desired); // DEBUG
fscanf(configfile, "%i", &selection);
printf("Selection/fitness value = %i\n", selection); // DEBUG
fscanf(configfile, "%s", outputfile);
printf("Output file = %s\n\n", outputfile); // DEBUG
fclose(configfile);
// load the pedigree
FILE* pedfile_handle = fopen(pedfile, "r");
if (pedfile_handle == NULL) {
printf("ERROR: No Such Pedigree\n");
exit(1);
}
// printf("Loading pedigree file.\n"); // DEBUG
int findivs[numHut];
int numAllele[numHut];
int* toMom[numHut];
int* toDad[numHut];
int i, j;
for (i = 0; i < numHut; i++) {
int findiv, m_findiv, f_findiv;
fscanf(pedfile_handle, "%i\t%i\t%i", &findiv, &m_findiv, &f_findiv);
findivs[i] = findiv;
toMom[i] = NULL;
toDad[i] = NULL;
for (j = 0; j < i; j++ ) {
if((m_findiv != 0) && (findivs[j] == m_findiv)) {
toMom[i] = &(numAllele[j]);
}
if((f_findiv != 0) && (findivs[j] == f_findiv)) {
toDad[i] = &(numAllele[j]);
}
}
}
fclose(pedfile_handle);
// load the cohorts
FILE* cohortfile_handle = fopen(cohortfile, "r");
if (cohortfile_handle == NULL) {
printf("ERROR: Birth cohort file doesn't exist\n");
exit(1);
}
// printf("Loading cohorts.\n"); // DEBUG
struct genocount cohort_counts[num_cohorts]; // store genotype counts for each cohort, where each genocount is an element in the array cohort_counts
// printf("Initialize cohort_counts.\n"); // DEBUG
for (i = 0; i < num_cohorts; i++) {
init_genocount( &cohort_counts[i] );
}
// printf("Zeroing out to_cohort.\n"); // DEBUG
struct genocount* to_cohort[numHut];
for (i=0; i<numHut; i++) { // zero out pointers
to_cohort[i] = NULL;
}
int myfindiv, mycohort;
while (fscanf(cohortfile_handle, "%d\t%d", &myfindiv, &mycohort) != EOF) {
if (mycohort != 0) {
for (i = 0; i < numHut; i++) {
if (findivs[i] == myfindiv) {
to_cohort[i] = &( cohort_counts[mycohort] ); // create pointer to
}
}
}
}
fclose(cohortfile_handle);
// FINISHED LOADING DATA AND SETTING UP STRUCTURES
// BEGIN SIMULATION
printf("\nBegin simulation\n");
FILE* outfile_handle = fopen(outputfile, "w");
if (outfile_handle == NULL) {
printf("ERROR: Could Not Open Output File\n");
exit(1);
}
fprintf(outfile_handle, "founder\tnhomwt\tnhet\tnhommut\tfreq2pq\tfreqprophet\n"); // DEBUG
int chosenFounderidx = 0;
for (chosenFounderidx=0; chosenFounderidx<numFounder; chosenFounderidx++) { // iterate over all founders
int chosenFounder = findivs[chosenFounderidx];
printf("Simulating for founder #%d %d\n", chosenFounderidx, chosenFounder);
// printf("set num_trials val.\n"); // DEBUG
int num_trials = 0;
for (num_trials=0; num_trials<num_desired; num_trials++) {
//set founder alleles
// printf("set founders.\n"); // DEBUG
for (i = 0; i < numFounder; i++) {
numAllele[i] = 0;
}
numAllele[chosenFounderidx] = 1;
// printf("set others.\n"); // DEBUG
// simulate the rest
for (i = numFounder; i < numHut; i++) {
/*if ((toMom[i]) == NULL) {
printf("no mom! %d\n", findivs[i]);
exit(1);
}
if ((toDad[i]) == NULL) {
printf("no dad! %d\n", findivs[i]);
exit(1);
}*/
int numMom = *(toMom[i]);
//printf("mom's stuff : %d\n", numMom);
int numDad = *(toDad[i]);
//printf("dad's stuff : %d\n", numMom);
numAllele[i] = randAllele(numMom, numDad, selection);
}
// printf("storing data.\n"); \\ DEBUG
// finished dropping alleles for this iterations, save informatino
// calculate frequency in current cohort
for (j = 0; j < numHut; j++) {
int findiv = findivs[j];
int mycount = numAllele[j];
if (to_cohort[j] != NULL) {
if (mycount == 0) {
to_cohort[j]->AA += 1;
}
else if (mycount == 1) {
to_cohort[j]->Aa += 1;
}
else if (mycount == 2) {
to_cohort[j]->aa += 1;
}
}
}
// print results to file // DEBUG
// printf("print results to output\n"); // DEBUG
float freq2pq = (cohort_counts[1].Aa + 2.0 * cohort_counts[1].aa)/(2.0*(cohort_counts[1].AA + cohort_counts[1].Aa + cohort_counts[1].aa));
float freqprop = (1.0 * cohort_counts[1].Aa)/(cohort_counts[1].AA + cohort_counts[1].Aa + cohort_counts[1].aa);
fprintf(outfile_handle, "%d\t%d\t%d\t%d\t%f\t%f\n", chosenFounder, cohort_counts[1].AA, cohort_counts[1].Aa, cohort_counts[1].aa, freq2pq, freqprop); // founderfindiv, number of hom_wt, het, hom_mutant
// reinitialize cohort_count storage
for (i = 0; i < num_cohorts; i++) {
init_genocount( &cohort_counts[i] );
}
}
}
fclose(outfile_handle);
exit(0);
}