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// Copyright 2013 Calvin Morrison
#include <errno.h>
#include <getopt.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 *fn = NULL;
FILE *fh = NULL;
// for specific mers
char *mer_fn = NULL;
size_t num_desired_indicies = 0;
size_t *desired_indicies = NULL;
// for getdelim
char *line = NULL;
size_t len = 0;
ssize_t read;
// sizes
unsigned int kmer = 0;
size_t width = 0;
bool sparse = false;
bool kmer_set = false;
bool specific_mers = false;
static struct option long_options[] = {
{"input", required_argument, 0, 'i'},
{"kmer", required_argument, 0, 'k'},
{"sparse", no_argument, 0, 's'},
{"mer-file", required_argument, 0, 'm'},
{"help", no_argument, 0, 'h'},
{0, 0, 0, 0}
};
while (1) {
int option_index = 0;
int c = 0;
c = getopt_long (argc, argv, "i:k:m:vsh", long_options, &option_index);
if (c == -1)
break;
switch (c) {
case 'i':
fn = optarg;
break;
case 'k':
kmer = atoi(optarg);
kmer_set = true;
break;
case 's':
sparse = true;
break;
case 'm':
mer_fn = optarg;
specific_mers = true;
break;
case 'h':
help();
exit(EXIT_SUCCESS);
break;
case 'v':
printf("dna-utils version " VERSION "\n");
exit(EXIT_SUCCESS);
break;
default:
break;
}
}
if(argc == 1) {
help();
exit(EXIT_FAILURE);
}
if(fn == NULL) {
fprintf(stderr, "no input file specified with -i, reading from stdin\n");
fh = stdin;
}
else {
fh = fopen(fn, "r");
if(fh == NULL) {
fprintf(stderr, "Could not open %s - %s\n", fn, strerror(errno));
exit(EXIT_FAILURE);
}
}
if(!kmer_set) {
fprintf(stderr, "Error: kmer (-k) must be supplied\n");
exit(EXIT_FAILURE);
}
if(kmer == 0) {
fprintf(stderr, "Error: invalid kmer - '%d'.\n", kmer);
exit(EXIT_FAILURE);
}
width = pow_four(kmer);
if(specific_mers) {
desired_indicies = malloc((width) * sizeof(size_t));
check_null_ptr(desired_indicies, NULL);
num_desired_indicies = load_specific_mers_from_file(mer_fn, kmer, width, desired_indicies);
if(num_desired_indicies == 0) {
fprintf(stderr, "Error: no mers loaded from file\n");
exit(EXIT_FAILURE);
}
}
unsigned long long *counts = malloc((width+ 1) * sizeof(unsigned long long));
if(counts == NULL) {
fprintf(stderr, "%s\n", strerror(errno));
exit(EXIT_FAILURE);
}
unsigned long long sequence = 0;
while ((read = getdelim(&line, &len, '>', fh)) != -1) {
long long i = 0;
size_t k = 0;
memset(counts, 0, width * sizeof(unsigned long long));
// find our first \n, this should be the end of the header
char *seq = strchr(line, '\n');
if(seq == NULL)
continue;
// point to one past that.
seq = seq + 1;
// strip out all other newlines to handle multiline sequences
size_t seq_length = strnstrip(seq, '\n', strlen(seq));
// reset our count matrix to zero
for(k = 0; k < seq_length; k++) {
seq[k] = alpha[(int)seq[k]];
}
for(i = 0; i < (signed long long)(seq_length - kmer + 1); i++) {
size_t mer = num_to_index(&seq[i],kmer, width, &i);
counts[mer]++;
}
if(specific_mers) {
for(k = 0; k < num_desired_indicies; k++) {
if(counts[desired_indicies[k]] != 0)
fprintf(stdout, "%llu\t%zu\t%llu\n", sequence, desired_indicies[k], counts[desired_indicies[k]]);
}
}
else if(sparse) {
for(k = 0; k < width; k++) {
if(counts[k] != 0)
fprintf(stdout, "%llu\t%zu\t%llu\n", sequence, k, counts[k]);
}
}
else {
for(k = 0; k < width - 1; k++)
fprintf(stdout, "%llu\t", counts[k]);
fprintf(stdout, "%llu\n", counts[width - 1]);
}
sequence++;
}
free(counts);
free(line);
free(desired_indicies);
fclose(fh);
return EXIT_SUCCESS;
}
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