diff options
Diffstat (limited to 'src/c/multifasta_to_otu.c')
| -rw-r--r-- | src/c/multifasta_to_otu.c | 19 |
1 files changed, 8 insertions, 11 deletions
diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c index aa9f821..9a9ee88 100644 --- a/src/c/multifasta_to_otu.c +++ b/src/c/multifasta_to_otu.c @@ -19,8 +19,6 @@ #include <sys/sysinfo.h> #endif -#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, --input-filelist\n\ta file containing list of fasta files to process seperated by newline (same rules apply as input-directory)\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." static int cmp (const void * a, const void * b) { @@ -353,6 +351,7 @@ int main(int argc, char **argv) { printf("processing %s\n", filenames[i]); file_sequence_count = count_sequences(filenames[i]); + printf("%s has %llu sequences\n", filenames[i], file_sequence_count); // load counts matrix double *count_matrix = malloc(width * sizeof(double)); @@ -365,7 +364,8 @@ int main(int argc, char **argv) { unsigned long long *integer_counts = get_kmer_counts_from_file(filenames[i], kmer); for(x = 0; x < width; x++) { - sorted_count_matrix[x] = count_matrix[x] = (double)integer_counts[x]; + count_matrix[x] = (double)integer_counts[x]; + sorted_count_matrix[x] = count_matrix[x]; } free(integer_counts); @@ -410,7 +410,7 @@ int main(int argc, char **argv) { // in both our count matrix and our sensing matrix // // y = 1 because we are offsetting the array by 1, so we can set the first row to all 1's - for(x = 0, y = 1; x < width - 1; x++) { + for(x = 0, y = 1; x < width; x++) { if(count_matrix[x] <= rare_value) { count_matrix_rare[y] = count_matrix[x]; @@ -421,6 +421,7 @@ int main(int argc, char **argv) { } } + // normalize our kmer counts and our sensing_matrix normalize_matrix(count_matrix_rare, 1, rare_width); normalize_matrix(sensing_matrix_rare, sequences, rare_width); @@ -443,15 +444,11 @@ int main(int argc, char **argv) { sensing_matrix_rare[x*rare_width] = 1.0; } - size_t zz; - for(y = 0; y < sequences; y++) { - for(zz = 0; zz < rare_width - 1; zz++) - printf("%lf\t", sensing_matrix_rare[rare_width * y + zz]); - printf("%lf\n", sensing_matrix_rare[rare_width * y + rare_width - 1]); - } - double *solution = nnls(sensing_matrix_rare, count_matrix_rare, sequences, rare_width); + // normalize our solution + normalize_matrix(solution, 1, sequences); + // add the current solution to the solutions array for(unsigned long long z = 0; z < sequences; z++ ) { solutions[sensing_matrix->sequences*i + z] = (unsigned long long)round(solution[z] * file_sequence_count); |