diff options
Diffstat (limited to 'src/c/multifasta_to_otu.c')
| -rw-r--r-- | src/c/multifasta_to_otu.c | 37 |
1 files changed, 25 insertions, 12 deletions
diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c index fcb0822..a18ca91 100644 --- a/src/c/multifasta_to_otu.c +++ b/src/c/multifasta_to_otu.c @@ -22,6 +22,10 @@ #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-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) { + return ( *(double*)a - *(double*)b ); + } + char **get_fasta_files(char *directory) { DIR *dh; @@ -246,52 +250,61 @@ int main(int argc, char **argv) { #pragma omp parallel for shared(solutions, sensing_matrix_ptr, width, done, sequences) for(size_t i = 0; i < dir_count; i++ ) { - unsigned long long x = 0; - unsigned long long y = 0; - unsigned long long z = 0; + size_t x = 0; + size_t y = 0; + size_t z = 0; unsigned long long file_sequence_count = 0; unsigned long long rare_value = 0; unsigned long long rare_width = 0; - double percentage = 1.0; double rare_percent = 1.0; char *full_filename = malloc(strlen(input_fasta_directory) + strlen(filenames[i]) + 2); check_malloc(full_filename, NULL); sprintf(full_filename, "%s/%s", input_fasta_directory, filenames[i]); - printf("%s\n", full_filename); + printf("processing %s\n", full_filename); file_sequence_count = count_sequences(full_filename); // load counts matrix double *count_matrix = malloc(width * sizeof(double)); check_malloc(count_matrix, NULL); + double *sorted_count_matrix = malloc(width * sizeof(double)); + check_malloc(sorted_count_matrix, NULL); + // convert our matrix into doubles { unsigned long long *integer_counts = get_kmer_counts_from_file(full_filename, kmer); - for(x = 0; x < width; x++) - count_matrix[x] = (double)integer_counts[x]; + for(x = 0; x < width; x++) { + sorted_count_matrix[x] = count_matrix[x] = (double)integer_counts[x]; + } free(integer_counts); } + // sort our array + qsort(sorted_count_matrix, width, sizeof(double), cmp); + // get our "rare" counts - while(1) { + for(y = 0; y < width; y++) { + double percentage = 0; + + rare_value = sorted_count_matrix[y]; rare_width = 0; for(x = 0; x < width; x++) { - if(count_matrix[x] < rare_value) { + if(count_matrix[x] <= rare_value) { rare_width++; } } - percentage = (float)rare_width / (float)width; + percentage = (double)rare_width / (double)width; if(percentage >= rare_percent) break; - - rare_value++; } + + free(sorted_count_matrix); if(verbose) printf("there are %llu values less than %llu\n", rare_width, rare_value); |