1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
|
// 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_total_count -i input_file -k kmer [-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"
" --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;
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'},
{"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:nlvh", 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 '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_kmer_counts_from_file(fh, kmer);
// 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++) {
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=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;
}
|
