void
test1d_resample (void)
{
size_t i;
int status = 0;
gsl_histogram *h;
gsl_ieee_env_setup ();
h = gsl_histogram_calloc_uniform (10, 0.0, 1.0);
gsl_histogram_increment (h, 0.1);
gsl_histogram_increment (h, 0.2);
gsl_histogram_increment (h, 0.2);
gsl_histogram_increment (h, 0.3);
{
gsl_histogram_pdf *p = gsl_histogram_pdf_alloc (10);
gsl_histogram *hh = gsl_histogram_calloc_uniform (100, 0.0, 1.0);
gsl_histogram_pdf_init (p, h);
for (i = 0; i < 100000; i++)
{
double u = urand();
double x = gsl_histogram_pdf_sample (p, u);
gsl_histogram_increment (hh, x);
}
for (i = 0; i < 100; i++)
{
double y = gsl_histogram_get (hh, i) / 2500;
double x, xmax;
size_t k;
double ya;
gsl_histogram_get_range (hh, i, &x, &xmax);
gsl_histogram_find (h, x, &k);
ya = gsl_histogram_get (h, k);
if (ya == 0)
{
if (y != 0)
{
printf ("%d: %g vs %g\n", (int) i, y, ya);
status = 1;
}
}
else
{
double err = 1 / sqrt (gsl_histogram_get (hh, i));
double sigma = fabs ((y - ya) / (ya * err));
if (sigma > 3)
{
status = 1;
printf ("%g vs %g err=%g sigma=%g\n", y, ya, err, sigma);
}
}
}
gsl_histogram_pdf_free (p) ;
gsl_histogram_free (hh);
gsl_test (status, "gsl_histogram_pdf_sample within statistical errors");
}
gsl_histogram_free (h);
}
//Run the generator
void RandPSSMGen::RunGenerator()
{
int c, i, j, k,l,m,q,w,z, curr_len;
double curr_depth;
double x, r;
int zeros=0;
double col_sum=0;
double firstDraw, secondDraw, thirdDraw, sum;
gsl_histogram* width_hist;
gsl_histogram_pdf* width_pdf;
gsl_histogram* depth_hist;
gsl_histogram_pdf* depth_pdf;
double invariant_cols[6];
double total_cols[6];
double invariant_prob[6];
double abszero_cells[6];
double total_cells[6];
double abszero_prob[6];
gsl_histogram* first_edge_hist;
gsl_histogram_pdf* first_edge_pdf;
gsl_histogram* first_inner_hist;
gsl_histogram_pdf* first_inner_pdf;
gsl_histogram* second_edge_hist[5];
gsl_histogram_pdf* second_edge_pdf[5];
gsl_histogram* second_inner_hist[5];
gsl_histogram_pdf* second_inner_pdf[5];
gsl_histogram* third_edge_hist[5];
gsl_histogram_pdf* third_edge_pdf[5];
gsl_histogram* third_inner_hist[5];
gsl_histogram_pdf* third_inner_pdf[5];
FILE* out;
bool edge;
double known_zeros=0, known_total=0;
double new_zeros=0, new_total=0;
out = fopen(outFN, "w");
if(out==NULL)
{ printf("Error: cannot open file named %s\n", outFN);
exit(1);
}
//How many random matrices?
printf("%d Matrices Will Be Generated\n", numRandomMats);
//Read in the matrices
printf("%d Matrices Read In\n", numMatrices);
//1) The first step is to read in the width distribution
width_hist = gsl_histogram_alloc(7); //7 places in the histogram
double width_range[8] = {3, 5, 8, 10, 12, 14, 16, 25};
gsl_histogram_set_ranges(width_hist, width_range, 8);
for(i=0; i<numMatrices; i++) {//Go through each matrix, adding size to histogram
gsl_histogram_increment(width_hist, (double)matrices[i]->len);
}
width_pdf= gsl_histogram_pdf_alloc(7);
gsl_histogram_pdf_init(width_pdf, width_hist);
//1.1) Find the sequence depth distribution
depth_hist = gsl_histogram_alloc(7); //20 places in the histogram
double depth_range[8] = {0,5,10,20,40,80,160,1000};
gsl_histogram_set_ranges(depth_hist, depth_range, 8);
for(i=0; i<numMatrices; i++) {//Go through each matrix, adding each column depth to histogram
for(j=0; j<matrices[i]->len; j++){
double sum=0;
for(k=0; k<B; k++){
sum += matrices[i]->n[j][k];
}
gsl_histogram_increment(depth_hist, sum);
}
}
depth_pdf = gsl_histogram_pdf_alloc(7);
gsl_histogram_pdf_init(depth_pdf, depth_hist);
//2) The second step is to find the probability of invariance given the position of the column
//Also find the probability of an absolute zero (not including the invariant columns)
for(i=0; i<6; i++) {
invariant_cols[i]=0;
total_cols[i]=0;
abszero_cells[i]=0;
total_cells[i]=0;
}
bool inv=false;
for(i=0; i<numMatrices; i++) {
curr_len = matrices[i]->len;
for(j=0; j<curr_len; j++){
//Is the column invariant?
inv = Invariant(matrices[i]->n[j], zeros);
//What column are we in?
z = WhatColumn(j, curr_len);
total_cols[z]++;
invariant_cols[z]+=inv;
//Find zeros in a variable column
if(!inv) {
total_cells[z]+=4;
abszero_cells[z]+=zeros;
}
known_total+=4; known_zeros+=zeros;
}
}
for(i=0; i<6; i++){
invariant_prob[i]=invariant_cols[i]/total_cols[i];
abszero_prob[i]=abszero_cells[i]/total_cells[i];
}
printf("Known Zeros: %lf\n", known_zeros/known_total);
//3) Fill the First, Second, and Third Draw Histograms.
first_edge_hist = gsl_histogram_alloc(5);
gsl_histogram_set_ranges_uniform (first_edge_hist, 0.0001, 0.99999);
first_inner_hist = gsl_histogram_alloc(5);
gsl_histogram_set_ranges_uniform (first_inner_hist, 0.0001, 0.99999);
for(i=0; i<5; i++){
second_edge_hist[i] = gsl_histogram_alloc(5);
gsl_histogram_set_ranges_uniform(second_edge_hist[i], 0.0001, 0.99999);
second_inner_hist[i] = gsl_histogram_alloc(5);
gsl_histogram_set_ranges_uniform(second_inner_hist[i], 0.0001, 0.99999);
}
for(i=0; i<5; i++){
third_edge_hist[i] = gsl_histogram_alloc(5);
gsl_histogram_set_ranges_uniform(third_edge_hist[i], 0.0001, 0.99999);
third_inner_hist[i] = gsl_histogram_alloc(5);
gsl_histogram_set_ranges_uniform(third_inner_hist[i], 0.0001, 0.99999);
}
for(i=0; i<numMatrices; i++) {
curr_len = matrices[i]->len;
for(j=0; j<curr_len; j++){
if(WhatColumn(j, curr_len)==0)
edge=true;
else
edge=false;
//Discard Invariant Columns
if(!Invariant(matrices[i]->n[j], zeros)) {
col_sum = SumColumn(matrices[i]->n[j]);
for(k=0; k<B; k++) {
//Update first draw distribution
firstDraw =matrices[i]->n[j][k];
if(firstDraw!=0){//Discard Zeros
if(edge)
gsl_histogram_increment(first_edge_hist, firstDraw/col_sum);
else
gsl_histogram_increment(first_inner_hist, firstDraw/col_sum);
}
//Update second draw distribution
for(l=0; l<B; l++){
if(l!=k) {
secondDraw = matrices[i]->n[j][l];
if(secondDraw!=0) {
if(edge)
gsl_histogram_increment(second_edge_hist[(int)floor((firstDraw/col_sum)*5)], secondDraw/col_sum);
else
gsl_histogram_increment(second_inner_hist[(int)floor((firstDraw/col_sum)*5)], secondDraw/col_sum);
}
sum = secondDraw + firstDraw;
//Update third draw distribution
for(m=0; m<B; m++){
if(m!=k && m!=l) {
thirdDraw = matrices[i]->n[j][m];
if(thirdDraw!=0) {
if(edge)
gsl_histogram_increment(third_edge_hist[(int)floor((sum/col_sum)*5)], thirdDraw/col_sum);
else
gsl_histogram_increment(third_inner_hist[(int)floor((sum/col_sum)*5)], thirdDraw/col_sum);
}
}
}
}
}
}
}
}
}
//Start the PDFs here
first_edge_pdf= gsl_histogram_pdf_alloc(5);
gsl_histogram_pdf_init(first_edge_pdf, first_edge_hist);
first_inner_pdf= gsl_histogram_pdf_alloc(5);
gsl_histogram_pdf_init(first_inner_pdf, first_inner_hist);
for(i=0; i<5; i++) {
second_edge_pdf[i]= gsl_histogram_pdf_alloc(5);
gsl_histogram_pdf_init(second_edge_pdf[i], second_edge_hist[i]);
second_inner_pdf[i]= gsl_histogram_pdf_alloc(5);
gsl_histogram_pdf_init(second_inner_pdf[i], second_inner_hist[i]);
}
for(i=0; i<5; i++) {
third_edge_pdf[i]= gsl_histogram_pdf_alloc(5);
gsl_histogram_pdf_init(third_edge_pdf[i], third_edge_hist[i]);
third_inner_pdf[i]= gsl_histogram_pdf_alloc(5);
gsl_histogram_pdf_init(third_inner_pdf[i], third_inner_hist[i]);
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////
//////// All information gathered... generating random samples from here on in /////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////////////
Motif* newPSSM = new Motif(31);
for(z=0; z<numRandomMats; z++) {
double r;
int base;
int first, second, third, fourth;
//first step: pick a length
r=((double)rand())/RAND_MAX;
curr_len = (int)gsl_histogram_pdf_sample(width_pdf, r);
if(curr_len>30){curr_len=30;}
for(i=0; i<curr_len; i++) { //Generate one column at a time
//Reset the column
for(j=0; j<B; j++)
newPSSM->f[i][j]=0;
if(WhatColumn(i, curr_len)==0)
edge=true;
else
edge=false;
//Is the column variable?
r=((double)rand())/RAND_MAX;
c = WhatColumn(i, curr_len);
if(r<invariant_prob[c]) { //The column has been chosen as invariant
//Which base is invariant?
r = ((double)rand())/RAND_MAX;
if(r<0.285){base=0;}
else if(r<0.57){base=3;}
else if(r<0.785){base=1;}
else{base=2;}
newPSSM->f[i][base]=1;
for(j=0; j<B; j++) {
if(j!=base)
newPSSM->f[i][j]=0;
}
}else{//the column has been chosen as variable
sum=0;
//Which base will be the focus of the first draw?
first = rand()%B;
//Is the first draw an absolute zero?
r=((double)rand())/RAND_MAX;
if(r<abszero_prob[WhatColumn(i, curr_len)]){//the cell is zero
newPSSM->f[i][first]=0;
}else{//the cell isn't zero
//Sample from the first cell pdf
r=((double)rand())/RAND_MAX;
if(edge)
newPSSM->f[i][first] = gsl_histogram_pdf_sample(first_edge_pdf, r);
else
newPSSM->f[i][first] = gsl_histogram_pdf_sample(first_inner_pdf, r);
}
sum+=newPSSM->f[i][first];
//Onto the second draw
second=rand()%B;
while(second==first)
{ second=rand()%B;}
r=((double)rand())/RAND_MAX;
if(r<abszero_prob[WhatColumn(i, curr_len)]){//the cell is zero
newPSSM->f[i][second]=0;
}else{//the cell isn't zero
//Sample from the first cell pdf
r=((double)rand())/RAND_MAX;
if(edge)
newPSSM->f[i][second] = gsl_histogram_pdf_sample(second_edge_pdf[(int)floor((sum)*5)], r);
else
newPSSM->f[i][second] = gsl_histogram_pdf_sample(second_inner_pdf[(int)floor((sum)*5)], r);
}
sum+=newPSSM->f[i][second];
//NORMALIZING! Check if anything is over 1 at this stage!
if(sum>1)
{ newPSSM->f[i][first] = newPSSM->f[i][first]/sum;
newPSSM->f[i][second] = newPSSM->f[i][second]/sum;
sum=1;
}else{
//Deal with the third draw here
third=rand()%B;
while(third==first || third==second)
{ third=rand()%B;}
r=((double)rand())/RAND_MAX;
if(r<abszero_prob[WhatColumn(i, curr_len)]){//the cell is zero
newPSSM->f[i][third]=0;
}else{//the cell isn't zero
//Sample from the first cell pdf
r=((double)rand())/RAND_MAX;
if(edge)
newPSSM->f[i][third] = gsl_histogram_pdf_sample(third_edge_pdf[(int)floor((sum)*5)], r);
else
newPSSM->f[i][third] = gsl_histogram_pdf_sample(third_inner_pdf[(int)floor((sum)*5)], r);
}
sum+=newPSSM->f[i][third];
//NORMALIZING! Check if anything is over 1 at this stage!
if(sum>1)
{ newPSSM->f[i][first] = newPSSM->f[i][first]/sum;
newPSSM->f[i][second] = newPSSM->f[i][second]/sum;
newPSSM->f[i][third] = newPSSM->f[i][third]/sum;
sum=1;
}else{
//Deal with the last base here
fourth=0;
while(fourth==first||fourth==second||fourth==third)
fourth++;
newPSSM->f[i][fourth]=1-sum;
}
}
}
Invariant(newPSSM->f[i], zeros);
new_total+=4; new_zeros+=zeros;
}
//PSSM Generated!
//Convert to n's
r=((double)rand())/RAND_MAX;
curr_depth = gsl_histogram_pdf_sample(depth_pdf, r);
if(curr_depth<5){curr_len=5;}
for(q=0; q<curr_len; q++){
for(w=0; w<B; w++){
newPSSM->n[q][w] = ceil(newPSSM->f[q][w]*curr_depth);
}
}
//Output in TRANSFAC format
fprintf(out, "DE\tRAND%d\n", z);
for(q=0; q<curr_len; q++){
fprintf(out, "%d\t%lf\t%lf\t%lf\t%lf\tX\n", q, newPSSM->n[q][0],newPSSM->n[q][1],newPSSM->n[q][2],newPSSM->n[q][3]);
}
fprintf(out, "XX\n");
}
printf("New Zeros: %lf\n", new_zeros/new_total);
/////////////////// Memory cleaning area ///////////////////////////////////////////////////////////////////
delete newPSSM;
gsl_histogram_free(width_hist);
gsl_histogram_pdf_free(width_pdf);
gsl_histogram_free(first_edge_hist);
gsl_histogram_pdf_free(first_edge_pdf);
gsl_histogram_free(first_inner_hist);
gsl_histogram_pdf_free(first_inner_pdf);
for(i=0; i<5; i++) {
gsl_histogram_free(second_edge_hist[i]);
gsl_histogram_pdf_free(second_edge_pdf[i]);
gsl_histogram_free(second_inner_hist[i]);
gsl_histogram_pdf_free(second_inner_pdf[i]);
}
for(i=0; i<5; i++) {
gsl_histogram_free(third_edge_hist[i]);
gsl_histogram_pdf_free(third_edge_pdf[i]);
gsl_histogram_free(third_inner_hist[i]);
gsl_histogram_pdf_free(third_inner_pdf[i]);
}
fclose(out);
}
