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
|
#include <ctype.h>
#include <errno.h>
#include <getopt.h>
#include <math.h>
#include <stdio.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include "nnls.h"
#include "quikr_functions.h"
#define sensing_matrix(i,j) (sensing_matrix[width*i + j])
#define USAGE "Usage:\n\tquikr [OPTION...] - Calculate estimated frequencies of bacteria in a sample.\n\nOptions:\n\n-i, --input\n\tthe sample's fasta file of NGS READS (fasta format)\n\n-f, --sensing-fasta\n\tlocation of the fasta file database used to create the sensing matrix (fasta format)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (trained from quikr_train)\n\n-k, --kmer\n\tspecify what size of kmer to use. (default value is 6)\n\n-l, --lambda\n\tlambda value to use. (default value is 10000)\n\n-o, --output\n\tOTU_FRACTION_PRESENT a vector representing the percentage of database sequence's presence in sample. (csv output)\n\n-v, --verbose\n\tverbose mode.\n\n-V, --version\n\tprint version."
int main(int argc, char **argv) {
int c;
char *input_fasta_filename = NULL;
char *sensing_matrix_filename = NULL;
char *sensing_fasta_filename = NULL;
char *output_filename = NULL;
long x = 0;
long y = 0;
int verbose = 0;
int debug = 0;
int lambda = 10000;
int kmer = 6;
long width = 0;
long sequences = 0;
while (1) {
static struct option long_options[] = {
{"input", required_argument, 0, 'i'},
{"kmer", required_argument, 0, 'k'},
{"lambda", required_argument, 0, 'l'},
{"output", required_argument, 0, 'o'},
{"sensing-fasta", required_argument, 0, 'f'},
{"sensing-matrix", required_argument, 0, 's'},
{"verbose", no_argument, 0, 'v'},
{"version", no_argument, 0, 'V'},
{"help", no_argument, 0, 'h'},
{"debug", no_argument, 0, 'd'},
{0, 0, 0, 0}
};
int option_index = 0;
c = getopt_long (argc, argv, "k:l:f:s:i:o:hdvV", long_options, &option_index);
if (c == -1)
break;
switch (c) {
case 'k':
kmer = atoi(optarg);
break;
case 'l':
lambda = atoi(optarg);
break;
case 'f':
sensing_fasta_filename = optarg;
break;
case 's':
sensing_matrix_filename = optarg;
break;
case 'i':
input_fasta_filename = optarg;
break;
case 'o':
output_filename = optarg;
break;
case 'v':
verbose = 1;
break;
case 'V':
printf("%s\n", VERSION);
exit(EXIT_SUCCESS);
break;
case 'h':
printf("%s\n", USAGE);
exit(EXIT_SUCCESS);
break;
default:
break;
}
}
if(sensing_matrix_filename == NULL) {
fprintf(stderr, "Error: sensing matrix filename (-s) must be specified\n\n");
fprintf(stderr, "%s\n", USAGE);
exit(EXIT_FAILURE);
}
if(sensing_fasta_filename == NULL) {
fprintf(stderr, "Error: sensing fasta filename (-f) must be specified\n\n");
fprintf(stderr, "%s\n", USAGE);
exit(EXIT_FAILURE);
}
if(output_filename == NULL) {
fprintf(stderr, "Error: output filename (-o) must be specified\n\n");
fprintf(stderr, "%s\n", USAGE);
exit(EXIT_FAILURE);
}
if(input_fasta_filename == NULL) {
fprintf(stderr, "Error: input fasta file (-i) must be specified\n\n");
fprintf(stderr, "%s\n", USAGE);
exit(EXIT_FAILURE);
}
if(verbose) {
printf("kmer: %d\n", kmer);
printf("lambda: %d\n", lambda);
printf("fasta: %s\n", input_fasta_filename);
printf("sensing database: %s\n", sensing_matrix_filename);
printf("sensing database fasta: %s\n", sensing_fasta_filename);
printf("output: %s\n", output_filename);
}
if(access (sensing_matrix_filename, F_OK) == -1) {
fprintf(stderr, "Error: could not find %s\n", sensing_matrix_filename);
exit(EXIT_FAILURE);
}
if(access (sensing_fasta_filename, F_OK) == -1) {
fprintf(stderr, "Error: could not find %s\n", sensing_fasta_filename);
exit(EXIT_FAILURE);
}
if(access (input_fasta_filename, F_OK) == -1) {
fprintf(stderr, "Error: could not find %s\n", input_fasta_filename);
exit(EXIT_FAILURE);
}
// 4 "ACGT" ^ Kmer gives us the size of output rows
width = pow(4, kmer);
width = width + 1;
sequences = count_sequences(sensing_fasta_filename);
if(sequences == 0) {
fprintf(stderr, "Error: %s contains 0 fasta sequences\n", sensing_fasta_filename);
}
if(verbose) {
printf("width: %ld\nsequences %ld\n", width, sequences);
}
double *sensing_matrix = load_sensing_matrix(sensing_matrix_filename, sequences, width);
double *count_matrix = load_count_matrix(input_fasta_filename, width, kmer);
// multiply our matrix by lambda
for(x = 1; x < sequences; x++) {
for(y= 0; y < width - 1; y++) {
sensing_matrix(x, y) = sensing_matrix(x, y) * lambda;
}
}
for(x = 0; x < sequences; x++) {
sensing_matrix(x, 0) = 1.0;
}
// normalize our count_matrix
normalize_matrix(count_matrix, 1, width);
for(x = 0; x < width; x++)
count_matrix[x] = count_matrix[x] * lambda;
double *solution = nnls(sensing_matrix, count_matrix, sequences, width);
// normalize our solution vector
normalize_matrix(solution, 1, sequences);
// output our matrix
FILE *output_fh = fopen(output_filename, "w");
if(output_fh == NULL) {
fprintf(stderr, "Could not open %s for writing\n", output_filename);
exit(EXIT_FAILURE);
}
for(x = 0; x < sequences; x++) {
fprintf(output_fh, "%.10lf\n", solution[x]);
}
fclose(output_fh);
return EXIT_SUCCESS;
}
|
