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// Copyright 2013 Calvin Morrison
#include <errno.h>
#include <stdbool.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <getopt.h>
#include "kmer_utils.h"
void help() {
printf("usage: kmer_continuous_count -i input_file -k kmer [-c] [-n] [-l] ...\n\n"
"count mers in size k from a fasta file, but do so continuously\n"
"\n"
" --input -i input fasta file to count\n"
" --kmer -k size of mers to count\n"
" --compliment -c count compliment of sequences\n"
" --nonzero -n only print non-zero values\n"
" --label -l print mer along with 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) {
char *fn = NULL;
FILE *fh = NULL;
unsigned int kmer = 0;
bool nonzero = false;
bool label = false;
bool kmer_set = false;
bool count_compliment = false;
unsigned long long width = 0;
unsigned long long i = 0;
static struct option long_options[] = {
{"input", required_argument, 0, 'i'},
{"kmer", required_argument, 0, 'k'},
{"compliment", required_argument, 0, 'c'},
{"nonzero", no_argument, 0, 'n'},
{"label", no_argument, 0, 'l'},
{"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:cnlvh", 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 'c':
count_compliment = true;
break;
case 'n':
nonzero = true;
break;
case 'l':
label = 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);
unsigned long long *counts = get_continuous_kmer_counts_from_file(fh, kmer, count_compliment);
// If nonzero is set, only print non zeros
if(nonzero) {
// if labels is set, print out our labels
if(label) {
for(i = 0; i < width; i++)
if(counts[i] != 0) {
char *kmer_str = index_to_kmer(i, kmer);
fprintf(stdout, "%s\t%llu\n", kmer_str, counts[i]);
free(kmer_str);
}
}
else {
for(i = 0; i < width; i++)
if(counts[i] != 0)
fprintf(stdout, "%llu\t%llu\n", i, counts[i]);
}
}
// If we aren't printing nonzeros print everything
else {
if(label) {
for(i = 0; i < width; i++) {
char *kmer_str = index_to_kmer(i, kmer);
fprintf(stdout, "%s\t%llu\n", kmer_str, counts[i]);
free(kmer_str);
}
}
else {
for(i = 0; i < width; i=i+4) {
fprintf(stdout, "%llu\n%llu\n%llu\n%llu\n", counts[i], counts[i+1], counts[i+2], counts[i+3]);
}
}
}
free(counts);
return EXIT_SUCCESS;
}
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