From 00e5701708abb6837982f9aa5d38117cc5bbaee6 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Tue, 29 Oct 2013 15:07:30 -0400
Subject: update quikr to work with internally parsed sensing matrix
---
src/c/quikr.c | 54 +++++++++++++++++-------------------------------------
1 file changed, 17 insertions(+), 37 deletions(-)
diff --git a/src/c/quikr.c b/src/c/quikr.c
index 8a238f6..0570acc 100644
--- a/src/c/quikr.c
+++ b/src/c/quikr.c
@@ -10,18 +10,17 @@
#include "nnls.h"
#include "kmer_utils.h"
#include "quikr_functions.h"
+#include "quikr.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;
@@ -33,7 +32,6 @@ int main(int argc, char **argv) {
int kmer = 6;
long width = 0;
- long sequences = 0;
while (1) {
static struct option long_options[] = {
@@ -64,9 +62,6 @@ int main(int argc, char **argv) {
case 'l':
lambda = atoi(optarg);
break;
- case 'f':
- sensing_fasta_filename = optarg;
- break;
case 's':
sensing_matrix_filename = optarg;
break;
@@ -98,11 +93,6 @@ int main(int argc, char **argv) {
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);
@@ -118,8 +108,7 @@ int main(int argc, char **argv) {
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("sensing matrix: %s\n", sensing_matrix_filename);
printf("output: %s\n", output_filename);
}
@@ -127,10 +116,6 @@ int main(int argc, char **argv) {
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);
@@ -145,16 +130,6 @@ int main(int argc, char **argv) {
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);
- }
-
-
// load counts matrix
unsigned long long *integer_counts = get_kmer_counts_from_file(input_fasta_filename, kmer);
@@ -173,25 +148,30 @@ int main(int argc, char **argv) {
count_matrix[x] = count_matrix[x] * lambda;
// load sensing matrix
- double *sensing_matrix = load_sensing_matrix(sensing_matrix_filename, sequences, width);
+ struct matrix *sensing_matrix = load_sensing_matrix(sensing_matrix_filename);
+ if(sensing_matrix->kmer != kmer) {
+ fprintf(stderr, "The sensing_matrix was trained with a different kmer than your requested kmer\n");
+ exit(EXIT_FAILURE);
+ }
+
// multiply our sensing 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 = 1; x < sensing_matrix->sequences; x++) {
+ for(y = 0; y < width - 1; y++) {
+ sensing_matrix->matrix[width*x + y] = sensing_matrix->matrix[width*x + y] * lambda;
}
- }
+ }
// set the first column of our sensing matrix to 0
- for(x = 0; x < sequences; x++) {
- sensing_matrix(x, 0) = 1.0;
+ for(x = 0; x < sensing_matrix->sequences; x++) {
+ sensing_matrix->matrix[width * x] = 1.0;
}
// run NNLS
- double *solution = nnls(sensing_matrix, count_matrix, sequences, width);
+ double *solution = nnls(sensing_matrix->matrix, count_matrix, sensing_matrix->sequences, width);
// normalize our solution vector
- normalize_matrix(solution, 1, sequences);
+ normalize_matrix(solution, 1, sensing_matrix->sequences);
// output our matrix
FILE *output_fh = fopen(output_filename, "w");
@@ -199,7 +179,7 @@ int main(int argc, char **argv) {
fprintf(stderr, "Could not open %s for writing\n", output_filename);
exit(EXIT_FAILURE);
}
- for(x = 0; x < sequences; x++) {
+ for(x = 0; x < sensing_matrix->sequences; x++) {
fprintf(output_fh, "%.10lf\n", solution[x]);
}
fclose(output_fh);
--
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