diff options
Diffstat (limited to 'src/c/multifasta_to_otu.c')
| -rw-r--r-- | src/c/multifasta_to_otu.c | 35 |
1 files changed, 8 insertions, 27 deletions
diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c index 72d13b5..fb64981 100644 --- a/src/c/multifasta_to_otu.c +++ b/src/c/multifasta_to_otu.c @@ -20,7 +20,7 @@ #define sensing_matrix(i,j) (sensing_matrix[width*i + j]) #define solutions(i,j) (solutions[sequences*i+ j]) -#define USAGE "Usage:\n\tmultifasta_to_otu [OPTION...] - create a QIIME OTU table based on Quikr results. \n\nOptions:\n\n-i, --input-directory\n\tthe directory containing the samples' fasta files of reads (note each file should correspond to a separate sample)\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. (sensing 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-j, --jobs\n\t specifies how many jobs to run at once. (default value is the number of CPUs)\n\n-o, --output\n\tthe OTU table, with NUM_READS_PRESENT for each sample which is compatible with QIIME's convert_biom.py (or a sequence table if not OTU's)\n\n-v, --verbose\n\tverbose mode.\n\n-V, --version\n\tprint version." +#define USAGE "Usage:\n\tmultifasta_to_otu [OPTION...] - create a QIIME OTU table based on Quikr results. \n\nOptions:\n\n-i, --input-directory\n\tthe directory containing the samples' fasta files of reads (note each file should correspond to a separate sample)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (sensing 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-j, --jobs\n\t specifies how many jobs to run at once. (default value is the number of CPUs)\n\n-o, --output\n\tthe OTU table, with NUM_READS_PRESENT for each sample which is compatible with QIIME's convert_biom.py (or a sequence table if not OTU's)\n\n-v, --verbose\n\tverbose mode.\n\n-V, --version\n\tprint version." int main(int argc, char **argv) { @@ -173,15 +173,15 @@ int main(int argc, char **argv) { } // multiply our matrix by lambda - for(x = 0; x < sensing_matrix->sequences; x++) { - for(y= 0; y < width; y++) { - sensing_matrix->matrix[x*width + 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 row to be all 1's for(x = 0; x < sensing_matrix->sequences; x++) { - sensing_matrix->matrix[x*width] = 1.0; + sensing_matrix->matrix[width * x] = 1.0; } double *solutions = malloc(dir_count * sensing_matrix->sequences * sizeof(double)); @@ -196,7 +196,7 @@ int main(int argc, char **argv) { exit(EXIT_FAILURE); } - long *file_sequence_count = malloc(dir_count * sizeof(long)); + long *file_sequence_count = calloc(dir_count, sizeof(long)); if(file_sequence_count == NULL) { fprintf(stderr, "Could not allocate enough memory\n"); exit(EXIT_FAILURE); @@ -237,27 +237,8 @@ int main(int argc, char **argv) { // get individual sequence count file_sequence_count[i] = count_sequences(filename); - // count the kmer amounts, and convert it to a double array - unsigned long long *integer_counts = get_kmer_counts_from_file(filename, kmer); - double *count_matrix = malloc(sizeof(double) * width); - if(count_matrix == NULL) { - fprintf(stderr, "Could not allocate memory:\n"); - exit(EXIT_FAILURE); - } - - count_matrix[0] = 0; - - for(x = 0; x < width - 1 ; x++) - count_matrix[x+1] = (double)integer_counts[x]; - - free(integer_counts); - - // normalize our kmer counts - normalize_matrix(count_matrix, 1, width); - - // multiply our kmers frequency by lambda - for(z = 0; z < width; z++) - count_matrix[z] = count_matrix[z] * lambda; + // get our count matrix + double *count_matrix = setup_count_matrix(filename, kmer, lambda, width); double *sensing_matrix_copy = malloc(sizeof(double) * sensing_matrix->sequences * width); if(sensing_matrix_copy == NULL) { |