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
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
|
// Copyright 2013 Calvin Morrison
#include <errno.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "kmer_total_count.h"
const unsigned char alpha[256] =
{5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 0, 5, 1, 5, 5, 5, 2,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5};
const char reverse_alpha[4] = { 'A', 'C', 'G', 'T' };
inline unsigned long long pow_four(unsigned long long x) {
return (unsigned long long)1 << (x * 2);
}
// convert a string of k-mer size base-4 values into a
// base-10 index
inline unsigned long num_to_index(const char *str, const int kmer, const long error_pos, size_t *current_position) {
int i = 0;
unsigned long out = 0;
unsigned long multiply = 1;
for(i = kmer - 1; i >= 0; i--){
if(str[i] == 5) {
current_position += i;
return error_pos;
}
out += str[i] * multiply;
multiply = multiply << 2;
}
return out;
}
// return the number of loaded elements
unsigned long long load_specific_mers_from_file(char *fn, unsigned int kmer, size_t width, size_t *arr) {
FILE *fh;
size_t arr_pos = 0;
char line[64];
fh = fopen(fn, "r");
if(fh == NULL) {
fprintf(stderr, "Error opening %s - %s\n", fn, strerror(errno));
exit(EXIT_FAILURE);
}
while (fgets(line, sizeof(line), fh) != NULL) {
size_t i;
size_t len;
len = strlen(line);
if(len == 0)
continue;
len--;
line[len] = '\0';
if(len != kmer) {
fprintf(stderr, "SKIPPING: '%s' is not length %u\n", line, kmer);
continue;
}
for(i = 0; i < len; i++) {
line[i] = alpha[(int)line[i]];
}
size_t mer = num_to_index(line, kmer, width, NULL);
if(mer == width) {
fprintf(stderr, "SKIPPING: '%s' is a unrecognized mer\n", line);
continue;
}
else {
arr[arr_pos] = mer;
arr_pos++;
}
}
fclose(fh);
return arr_pos;
}
// convert an index back into a kmer string
char *index_to_kmer(unsigned long long index, long kmer) {
size_t i = 0;
size_t j = 0;
char *num_array = calloc(kmer, sizeof(char));
char *ret = calloc(kmer + 1, sizeof(char));
if(ret == NULL)
exit(EXIT_FAILURE);
// this is the core of the conversion. modulus 4 for base 4 conversion
while (index != 0) {
num_array[i] = index % 4;
index /= 4;
i++;
}
// for our first few nmers, like AAAAA, the output would only be "A" instead
// of AAAAA so we prepend it
for(j = 0; j < (kmer - i); j++)
ret[j] = 'A';
// our offset for how many chars we prepended
int offset = j;
// save i so we can print it
size_t start = i ;
// decrement i by 1 to reverse the last i++
i--;
j = 0;
// reverse the array, as j increases, decrease i
for(j = 0; j < start; j++, i--)
ret[j + offset] = reverse_alpha[(int)num_array[i]];
// set our last character to the null termination byte
ret[kmer + 1] = '\0';
free(num_array);
return ret;
}
// Strip out any character 'c' from char array 's' into a destination dest (you
// need to allocate that) and copy only len characters.
char *strnstrip(const char *s, char *dest, int c, unsigned long long len) {
unsigned long long i = 0;
unsigned long long j = 0;
for(i = 0; i < len; i++) {
if(s[i] != c) {
dest[j] = s[i];
j++;
}
}
dest[j] = '\0';
return dest;
}
unsigned long long * get_kmer_counts_from_file(const char *fn, const unsigned int kmer) {
char *line = NULL;
size_t len = 0;
ssize_t read;
size_t i = 0;
size_t position = 0;
FILE * const fh = fopen(fn, "r");
if(fh == NULL) {
fprintf(stderr, "Error opening %s - %s\n", fn, strerror(errno));
exit(EXIT_FAILURE);
}
// width is 4^kmer
// there's a sneaky bitshift to avoid pow dependency
const unsigned long width = pow_four(kmer);
// malloc our return array
unsigned long long * counts = calloc((width+ 1), sizeof(unsigned long long));
if(counts == NULL) {
fprintf(stderr, strerror(errno));
exit(EXIT_FAILURE);
}
char *str = malloc(4096);
if(str == NULL) {
fprintf(stderr, strerror(errno));
exit(EXIT_FAILURE);
}
unsigned long long str_size = 4096;
while ((read = getdelim(&line, &len, '>', fh)) != -1) {
// 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);
// relace A, C, G and T with 0, 1, 2, 3 respectively
// everything else is 5
for(i = 0; i < seq_length; i++) {
str[i] = alpha[(int)str[i]];
}
// loop through our string to process each k-mer
for(position = 0; position < (seq_length - kmer + 1); position++) {
unsigned long mer = 0;
unsigned 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(str[i] == 5) {
mer = width;
position = i;
goto next;
}
// multiply this char in the mer by the multiply
// and bitshift the multiply for the next round
mer += str[i] * multiply;
multiply = multiply << 2;
}
// use this point to get mer of our loop
next:
// bump up the mer value in the counts array
counts[mer]++;
}
}
free(line);
free(str);
fclose(fh);
return counts;
}
|
