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// Copyright 2013 Calvin Morrison
#include <errno.h>
#include <stdbool.h>
#include <cstdio>
#include <cstdlib>
#include <string.h>
#include <getopt.h>
#include "kmer_utils.h"
template <typename array_type>
void count_sequence(const char *seq, const size_t seq_length, const unsigned int kmer, array_type *counts) {
long long position;
long long i;
// loop through our seq to process each k-mer
for(position = 0; position < (signed)(seq_length - kmer + 1); position++) {
unsigned long long mer = 0;
unsigned long long multiply = 1;
// for each char in the k-mer check if it is an error char
for(i = position + kmer - 1; i >= position; i--){
if(seq[i] == 5) {
position = i;
goto next;
}
// multiply this char in the mer by the multiply
// and bitshift the multiply for the next round
mer += seq[i] * multiply;
multiply = multiply << 2;
}
// bump up the mer value in the counts array
inc(counts, mer);
// skip count if error
next: ;
}
}
void help() {
printf("usage: kmer_total_count -i input_file -k kmer [-c] [-n] [-l] ...\n\n"
"count mers in size k from a fasta file\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"
" --sparse -s force sparse table for any mer\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;
bool force_sparse = false;
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'},
{"sparse", no_argument, 0, 's'},
{"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:cnslvh", 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 's':
force_sparse = 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);
}
if(kmer > 12 || force_sparse) {
kmer_map *counts = NULL;
kmer_map *res = get_kmer_counts_from_file(counts, fh, kmer, count_compliment);
print_kmer(res, label, nonzero, kmer);
}
else {
unsigned long long *counts = NULL;
unsigned long long *res = get_kmer_counts_from_file(counts, fh, kmer, count_compliment);
print_kmer(res, label, nonzero, kmer);
}
return EXIT_SUCCESS;
}
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