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// Copyright 2013 Calvin Morrison
#include <errno.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdbool.h>
#include "kmer_utils.h"
void help() {
printf("usage: kmer_counts_per_sequence input_file kmer [kmer-file] ...\n\n"
"count mers in each sequence of size k from a fasta file\n"
"\n"
" --input -i input fasta file to count\n"
" --kmer -k size of mers to count\n"
" --mer-file -m a file containing a list of mers you are interested\n"
" in opening. this will enable output your results in\n"
" a sparse format \n"
" --sparse -s output values in a sparse format. output is in the\n"
" order sequence_number, mer_index, value\n"
"\n"
"Report all bugs to mutantturkey@gmail.com\n"
"\n"
"Copyright 2014 Calvin Morrison, Drexel University.\n"
"\n"
"If you are using any dna-utils tool for a publication\n"
"please cite your usage:\n\n"
"dna-utils. Drexel University, Philadelphia USA, 2014;\n"
"software available at www.github.com/EESI/dna-utils/\n");
}
int main(int argc, char **argv) {
// getdelim variables
char *line = NULL;
size_t len = 0;
ssize_t read;
// specific mer variables
bool specific_mers = false;
size_t num_desired_indicies = 0;
size_t *desired_indicies = NULL;
if(argc < 3) {
printf("Please supply a filename and a kmer\n");
exit(EXIT_FAILURE);
}
unsigned long kmer = atoi(argv[2]);
if(kmer == 0) {
fprintf(stderr, "Error: invalid kmer.\n");
exit(EXIT_FAILURE);
}
const unsigned long long width = (unsigned long long)1 << (kmer * 2);
if(argc == 4) {
specific_mers = true;
desired_indicies = malloc((width) * sizeof(size_t));
if(desired_indicies == NULL)
exit(EXIT_FAILURE);
num_desired_indicies = load_specific_mers_from_file(argv[3], kmer, width, desired_indicies);
}
FILE *fh = fopen(argv[1], "r" );
if(fh == NULL) {
fprintf(stderr, "Error opening %s - %s\n", argv[1], strerror(errno));
exit(EXIT_FAILURE);
}
unsigned long long *counts = malloc((width+ 1) * sizeof(unsigned long long));
if(counts == NULL)
exit(EXIT_FAILURE);
char *str = malloc(BUFSIZ);
if(str == NULL) {
fprintf(stderr, strerror(errno));
exit(EXIT_FAILURE);
}
unsigned long long str_size = BUFSIZ;
unsigned long long sequence = 0;
while ((read = getdelim(&line, &len, '>', fh)) != -1) {
size_t i = 0;
memset(counts, 0, width * sizeof(unsigned long long));
// find our first \n, this should be the end of the header
char *start = strchr(line, '\n');
if(start == NULL)
continue;
// point to one past that.
start = start + 1;
size_t start_len = strlen(start);
// if our current str buffer isn't big enough, realloc
if(start_len + 1 > str_size + 1) {
str = realloc(str, start_len + 1);
if(str == NULL) {
exit(EXIT_FAILURE);
fprintf(stderr, strerror(errno));
}
}
// strip out all other newlines to handle multiline sequences
str = strnstrip(start, str, '\n',start_len);
size_t seq_length = strlen(str);
// reset our count matrix to zero
for(i = 0; i < seq_length; i++) {
str[i] = alpha[(int)str[i]];
}
for(i = 0; i < (seq_length - kmer + 1); i++) {
size_t mer = num_to_index(&str[i],kmer, width, &i);
counts[mer]++;
}
if(specific_mers) {
for(i = 0; i < num_desired_indicies; i++)
printf("%llu\t%zu\t%llu\n", sequence, desired_indicies[i], counts[desired_indicies[i]]);
sequence++;
}
else {
for(i = 0; i < width - 1; i++)
printf("%llu\t", counts[i]);
printf("%llu\n", counts[width - 1]);
}
}
free(counts);
free(line);
return EXIT_SUCCESS;
}
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