diff options
| -rw-r--r-- | src/c/multifasta_to_otu.1 | 5 | ||||
| -rw-r--r-- | src/c/multifasta_to_otu.c | 39 |
2 files changed, 36 insertions, 8 deletions
diff --git a/src/c/multifasta_to_otu.1 b/src/c/multifasta_to_otu.1 index d261351..2825135 100644 --- a/src/c/multifasta_to_otu.1 +++ b/src/c/multifasta_to_otu.1 @@ -13,6 +13,8 @@ multifasta_to_otu \- create a QIIME OTU table based on Quikr results. .IR kmer ] .RB [ \-l .IR lambda ] +.RB [ \-r +.IR rare-percent ] .RB [ \-j .IR jobs ] .RB [ \-o @@ -43,6 +45,9 @@ specify what size of kmer to use. (default value is 6) .B \-l, --lambda lambda value to use. (default value is 10000) .TP +.B \-r, --rare-percent +remove mers from classification if their values are less than the x percentile of values in the sample (default value is 10000) +.TP .B \-j, --jobs specifies how many jobs to run at once. (default value is the number of CPUs) .TP diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c index 1ae1802..d5021fa 100644 --- a/src/c/multifasta_to_otu.c +++ b/src/c/multifasta_to_otu.c @@ -19,7 +19,31 @@ #include <sys/sysinfo.h> #endif -#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." +void usage() { + + printf("Usage: multifasta_to_otu [OPTION...] - create a QIIME OTU table based on Quikr results. \n\n" + "Options:\n\n" + "-i, --input-directory\n" + " the directory containing the samples' fasta files of reads (note each file should correspond to a separate sample)\n\n" + "-f,--input-filelist\n" + " a file containing list of fasta files to process seperated by newline (same rules apply as input-directory)\n\n" + "-s, --sensing-matrix\n" + " location of the sensing matrix. (sensing from quikr_train)\n\n" + "-k,--kmer\n" + " specify what size of kmer to use. (default value is 6)\n\n" + "-l,--lambda\n" + " lambda value to use. (default value is 10000)\n\n" + "-r,--rare-percent\n" + " remove mers from classification if their values are less than the x percentile of values in the sample (default value is 10000)\n\n" + "-j, --jobs\n" + " specifies how many jobs to run at once. (default value is the number of CPUs)\n\n" + "-o, --output\n" + " the 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" + " verbose mode.\n\n" + "-V, --version\n" + " print version.\n"); +} char **get_fasta_files_from_file(char *fn) { char **files; @@ -233,7 +257,7 @@ int main(int argc, char **argv) { exit(EXIT_SUCCESS); break; case 'h': - puts(USAGE); + usage(); exit(EXIT_SUCCESS); break; default: @@ -243,26 +267,26 @@ int main(int argc, char **argv) { if(sensing_matrix_filename == NULL) { fprintf(stderr, "Error: sensing matrix filename (-s) must be specified\n\n"); - fprintf(stderr, "%s\n", USAGE); + usage(); exit(EXIT_FAILURE); } if(output_filename == NULL) { fprintf(stderr, "Error: output filename (-o) must be specified\n\n"); - fprintf(stderr, "%s\n", USAGE); + usage(); exit(EXIT_FAILURE); } // input fasta parsing if(input_fasta_directory == NULL && input_fasta_filelist == NULL) { fprintf(stderr, "Error: input fasta directory (-i) or input fasta filelist (-f) must be specified\n\n"); - fprintf(stderr, "%s\n", USAGE); + usage(); exit(EXIT_FAILURE); } if(input_fasta_directory != NULL && input_fasta_filelist != NULL) { fprintf(stderr, "Error: input fasta directory (-i) and input fasta filelist (-f) cannot be used concurrently\n\n"); - fprintf(stderr, "%s\n", USAGE); + usage(); exit(EXIT_FAILURE); } @@ -273,6 +297,7 @@ int main(int argc, char **argv) { if(verbose) { printf("kmer: %u\n", kmer); + printf("rare: %lf\n", rare_percent); printf("lambda: %llu\n", lambda); printf("input directory: %s\n", input_fasta_directory); printf("input filelist: %s\n", input_fasta_filelist); @@ -343,8 +368,6 @@ int main(int argc, char **argv) { unsigned long long rare_value = 0; unsigned long long rare_width = 0; - double rare_percent = 1.0; - printf("processing %s\n", filenames[i]); file_sequence_count = count_sequences(filenames[i]); printf("%s has %llu sequences\n", filenames[i], file_sequence_count); |