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
|
#include <ctype.h>
#include <errno.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <zlib.h>
#include "quikr.h"
unsigned long long count_sequences(const char *filename) {
char *line = NULL;
size_t len = 0;
ssize_t read;
unsigned long long sequences = 0;
FILE *fh = fopen(filename, "r");
if(fh == NULL) {
fprintf(stderr, "could not open\"%s\"", filename );
exit(EXIT_FAILURE);
}
while ((read = getline(&line, &len, fh)) != -1) {
if(line[0] == '>')
sequences++;
}
free(line);
fclose(fh);
return sequences;
}
void normalize_matrix(double *matrix, long height, long width) {
long x = 0;
long y = 0;
for(x = 0; x < height; x++) {
double row_sum = 0;
for(y = 0; y < (width); y++)
row_sum = row_sum + matrix[width * x + y];
for(y = 0; y < (width); y++)
matrix[width * x + y] = matrix[width * x + y] / row_sum;
}
}
double *load_count_matrix(const char *filename, const long width, const int kmer) {
double *count_matrix = malloc(width*sizeof(double));
char count_command[1024];
long x = 0;
char *line = NULL;
size_t len = 0;
if(count_matrix == NULL) {
fprintf(stderr, "could not allocate enough memory for the count matrix\n");
exit(EXIT_FAILURE);
}
// create out count matrix
sprintf(count_command, "count-kmers -r %d -1 -u %s", kmer, filename);
FILE *count_output = popen(count_command, "r");
if(count_output == NULL) {
fprintf(stderr, "could not execute \"%s\"", count_command);
exit(EXIT_FAILURE);
}
// set first element to zero.
count_matrix[0] = 0;
// get our first line
getline(&line, &len, count_output);
count_matrix[1] = atoi(line);
// iterate over the rest of the lines
for(x = 2; x < width; x++) {
getline(&line, &len, count_output);
count_matrix[x] = atoi(line);
}
free(line);
pclose(count_output);
return count_matrix;
}
struct sensing_matrix *load_sensing_matrix(const char *filename) {
char *line = NULL;
char **headers = NULL;
double *matrix = NULL;
int kmer = 0;
unsigned long long i = 0;
unsigned long long *row = NULL;
unsigned long long sequences = 0;
unsigned long long width = 0;
struct matrix *ret = NULL;
gzFile fh = NULL;
fh = gzopen(filename, "r");
if(fh == NULL) {
fprintf(stderr, "could not open %s", filename);
exit(EXIT_FAILURE);
}
line = malloc(1024 * sizeof(char));
if(line == NULL)
exit(EXIT_FAILURE);
// Check for quikr
line = gzgets(fh, line, 1024);
if(strcmp(line, "quikr\n") != 0) {
fprintf(stderr, "This does not look like a quikr sensing matrix. Please check your path\n");
exit(EXIT_FAILURE);
}
// check version
line = gzgets(fh, line, 1024);
if(atoi(line) != MATRIX_REVISION) {
fprintf(stderr, "Sensing Matrix uses an unsupported version, please retrain your matrix\n");
exit(EXIT_FAILURE);
}
// get number of sequences
line = gzgets(fh, line, 1024);
sequences = strtoull(line, NULL, 10);
if(sequences == 0) {
fprintf(stderr, "Error parsing sensing matrix, please retrain your matrix\n");
exit(EXIT_FAILURE);
}
// get kmer
gzgets(fh, line, 1024);
kmer = atoi(line);
if(kmer == 0) {
fprintf(stderr, "Error parsing sensing matrix, please retrain your matrix\n");
exit(EXIT_FAILURE);
}
width = pow_four(kmer);
// allocate a +1 size for the extra row
matrix = malloc(sequences * (width + 1) * sizeof(double));
if(matrix == NULL) {
fprintf(stderr, "Could not allocate memory for the sensing matrix\n");
}
row = malloc(width * sizeof(unsigned long long));
if(row == NULL) {
fprintf(stderr, "Could not allocate memory for parsing row\n");
}
headers = malloc(sequences * sizeof(char *));
if(headers == NULL) {
fprintf(stderr, "could not allocated enough memory\n");
exit(EXIT_FAILURE);
}
for(i = 0; i < sequences; i++) {
unsigned long long sum = 0;
unsigned long long j = 0;
// get header and add it to headers array
char *header = malloc(256 * sizeof(char));
gzgets(fh, header, 256);
headers[i] = header+1;
for(j = 0; j < width; j++) {
line = gzgets(fh, line, 32);
if(line == NULL || line[0] == '>') {
fprintf(stderr, "Error parsing sensing matrix, please retrain your matrix\n");
exit(EXIT_FAILURE);
}
row[j] = strtoull(line, NULL, 10);
if(errno)
exit(EXIT_FAILURE);
sum += row[j];
}
for(j = 1; j < width+1; j++) {
matrix[i*width + j] = ((double)row[j-1]) / sum;
}
}
// load the matrix of counts
gzclose(fh);
free(line);
free(row);
ret = malloc(sizeof(struct matrix));
(*ret).kmer = kmer;
(*ret).sequences = sequences;
(*ret).matrix = matrix;
(*ret).headers = headers;
return ret;
}
char **load_headers(char *filename, long sequences) {
char command[512];
char *line= NULL;
long x = 0;
FILE *grep_output;
size_t len = 0;
sprintf(command, "grep ^\\> %s", filename);
grep_output = popen(command, "r");
if(grep_output == NULL) {
fprintf(stderr, "Could not execute %s\n", command);
exit(EXIT_FAILURE);
}
char **headers = malloc(sequences * sizeof(char *));
if(headers == NULL) {
fprintf(stderr, "could not allocated enough memory\n");
exit(EXIT_FAILURE);
}
for(x = 0; x < sequences; x++) {
char *header = malloc(256 * sizeof(char));
if(header == NULL) {
fprintf(stderr, "could not allocated enough memory\n");
exit(EXIT_FAILURE);
}
getline(&line, &len, grep_output);
sscanf(line + 1, "%s", header);
headers[x] = header;
}
free(line);
pclose(grep_output);
return headers;
}
|
