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#include <ctype.h>
#include <errno.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <zlib.h>
#include "kmer_utils.h"
#include "quikr.h"
void check_malloc(void *ptr, char *error) {
if (ptr == NULL) {
if(error != NULL) {
fprintf(stderr,"Error: %s\n", error);
}
else { fprintf(stderr, "Error: Could not allocate enough memory - %s\n", strerror(errno));
}
exit(EXIT_FAILURE);
}
}
void debug_arrays(double *count_matrix, struct matrix *sensing_matrix) {
FILE *count_fh = fopen("count.mat", "w");
FILE *sensing_fh = fopen("sensing.mat", "w");
unsigned long long width = pow_four(sensing_matrix->kmer);
unsigned long long i = 0;
unsigned long long j = 0;
for(i = 0; i < sensing_matrix->sequences; i++) {
for(j = 0; j < width - 1; j++)
fprintf(sensing_fh, "%lf\t", sensing_matrix->matrix[width*i + j]);
fprintf(sensing_fh, "%lf\n", sensing_matrix->matrix[width*i + width-1]);
}
fclose(sensing_fh);
for(j = 0; j < width - 1; j++)
fprintf(count_fh, "%lf\t", count_matrix[j]);
fprintf(count_fh, "%lf\n", count_matrix[width - 1]);
fclose(count_fh);
}
void normalize_matrix(double *matrix, unsigned long long height, unsigned long long width) {
unsigned long long x = 0;
unsigned long long y = 0;
for(x = 0; x < height; x++) {
double row_sum = 0;
for(y = 0; y < (width); y++)
row_sum = row_sum + matrix[width * x + y];
for(y = 0; y < (width); y++)
matrix[width * x + y] = matrix[width * x + y] / row_sum;
}
}
double *setup_count_matrix(char *filename, unsigned long long kmer, unsigned long long lambda, unsigned long long width) {
unsigned long long x = 0;
unsigned long long *integer_counts = get_kmer_counts_from_file(filename, kmer);
double *count_matrix = malloc(width * sizeof(double));
check_malloc(count_matrix, NULL);
count_matrix[0] = 0;
for(x = 1; x < width; x++) {
count_matrix[x] = (double)integer_counts[x-1];
}
free(integer_counts);
return count_matrix;
}
unsigned long long count_sequences(const char *filename) {
char *line = NULL;
size_t len = 0;
ssize_t read;
unsigned long long sequences = 0;
FILE *fh = fopen(filename, "r");
if(fh == NULL) {
fprintf(stderr, "could not open \"%s\"\n", filename );
return 0;
}
while ((read = getline(&line, &len, fh)) != -1) {
if(line[0] == '>')
sequences++;
}
free(line);
fclose(fh);
return sequences;
}
struct matrix *load_sensing_matrix(const char *filename, unsigned int target_kmer) {
char *line = NULL;
char **headers = NULL;
double *matrix = NULL;
int kmer = 0;
unsigned long long i = 0;
unsigned long long *row = NULL;
unsigned long long sequences = 0;
unsigned long long width = 0;
struct matrix *ret = NULL;
gzFile fh = NULL;
fh = gzopen(filename, "r");
if(fh == NULL) {
fprintf(stderr, "could not open %s", filename);
exit(EXIT_FAILURE);
}
line = malloc(1024 * sizeof(char));
check_malloc(line, NULL);
// Check for quikr
line = gzgets(fh, line, 1024);
if(strcmp(line, "quikr\n") != 0) {
fprintf(stderr, "This does not look like a quikr sensing matrix. Please check your path: %s\n", filename);
exit(EXIT_FAILURE);
}
// check version
line = gzgets(fh, line, 1024);
if(atoi(line) != MATRIX_REVISION) {
fprintf(stderr, "Sensing Matrix uses an unsupported version, please retrain your matrix\n");
exit(EXIT_FAILURE);
}
// get number of sequences
line = gzgets(fh, line, 1024);
sequences = strtoull(line, NULL, 10);
if(sequences == 0) {
fprintf(stderr, "Error parsing sensing matrix, sequence count is zero\n");
exit(EXIT_FAILURE);
}
// get kmer
gzgets(fh, line, 1024);
kmer = atoi(line);
if(kmer == 0) {
fprintf(stderr, "Error parsing sensing matrix, kmer is zero\n");
exit(EXIT_FAILURE);
}
if(kmer != target_kmer) {
fprintf(stderr, "The sensing_matrix was trained with a different kmer than your requested kmer\n");
exit(EXIT_FAILURE);
}
width = pow_four(kmer);
// allocate a +1 size for the extra row
matrix = malloc(sequences * (width) * sizeof(double));
check_malloc(matrix, NULL);
row = malloc((width) * sizeof(unsigned long long));
check_malloc(row, NULL);
headers = malloc(sequences * sizeof(char *));
check_malloc(headers, NULL);
for(i = 0; i < sequences; i++) {
unsigned long long j = 0;
// get header and add it to headers array
char *header = malloc(256 * sizeof(char));
check_malloc(header, NULL);
gzgets(fh, header, 256);
if(header[0] != '>') {
fprintf(stderr, "Error parsing sensing matrix, could not read header\n");
exit(EXIT_FAILURE);
}
header[strlen(header) - 1] = '\0';
headers[i] = header+1;
row = memset(row, 0, (width) * sizeof(unsigned long long));
for(j = 0; j < width; j++) {
line = gzgets(fh, line, 32);
if(line == NULL || line[0] == '>') {
fprintf(stderr, "Error parsing sensing matrix, line does not look like a value\n");
exit(EXIT_FAILURE);
}
row[j] = strtoull(line, NULL, 10);
if(errno) {
printf("could not parse '%s'\n into a number", line);
exit(EXIT_FAILURE);
}
}
for(j = 0; j < width; j++) {
matrix[i*(width) + j] = ((double)row[j]);
}
}
// load the matrix of counts
gzclose(fh);
free(line);
free(row);
ret = malloc(sizeof(struct matrix));
(*ret).kmer = kmer;
(*ret).sequences = sequences;
(*ret).matrix = matrix;
(*ret).headers = headers;
return ret;
}
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