2 files changed, 231 insertions, 143 deletions

diff --git a/src/c/kmer_utils.c b/src/c/kmer_utils.c
index 0980a69..4926788 100644
--- a/src/c/kmer_utils.c
+++ b/src/c/kmer_utils.c
@@ -59,6 +59,7 @@ char *strnstrip(const char *s, char *dest, int c, unsigned long long len) {
 	return dest;
 }
 
+
 unsigned long long * get_kmer_counts_from_file(const char *fn, const unsigned int kmer) {
 	
   char *line = NULL;
diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c
index 1abe787..e060fcf 100644
--- a/src/c/multifasta_to_otu.c
+++ b/src/c/multifasta_to_otu.c
@@ -23,28 +23,86 @@
 #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 );
-	 }
+	return ( *(double*)a - *(double*)b );
+}
+
+char **get_fasta_files_from_file(char *fn) {
+	char **files;
+	int files_count = 0;
+	
+	// getline stuff
+	ssize_t read;
+	size_t len = 0;
+	char *line = NULL;
+
+  FILE *fh = fopen(fn, "r");
+  if(fh == NULL) {
+    fprintf(stderr, "Error opening %s - %s\n", fn, strerror(errno));
+    exit(EXIT_FAILURE);
+  }
+
+	files = malloc(sizeof(char **));
+
+	while ((read = getline(&line, &len, fh)) != -1) {
+		char *file = malloc(sizeof(char) * (strlen(line)));	
+		if(file == NULL) {
+			exit(EXIT_FAILURE);
+		}
+		strncpy(file, line, strlen(line) + 1 );
+		printf("%zu\n", strlen(line));
+		printf("%zu\n", strlen(file));
+		file[strlen(file)- 1] = '\0';
+		printf(">%s< %zu >%s< %zu\n", line, strlen(line), file, strlen(file));
+	
+		if(access(file, F_OK) == 0) {
+
+			files[files_count] = file;
+			files_count++;
+
+			files = realloc(files, sizeof(char *) * (files_count + 1));
+			if(files == NULL) {
+				fprintf(stderr, "could not realloc keys\n");
+				exit(EXIT_FAILURE);
+			}
+		} 
+		else {
+			fprintf(stderr, "Warning: ignoring %s (%s)\n", file, strerror(errno)); 
+			errno = 0;
+			free(file);
+		}
+	}
 
-char **get_fasta_files(char *directory) {
+	files_count++;
+	files = realloc(files, sizeof(char *) * files_count);
+	if(files == NULL) {
+		fprintf(stderr, "could not realloc keys\n");
+		exit(EXIT_FAILURE);
+	}
+	files[files_count] = NULL;
+	
+	fclose(fh);
+	return files;
+}
+
+char **get_fasta_files_from_directory(char *directory) {
 
-  DIR *dh;
-  struct dirent *e;
+	DIR *dh;
+	struct dirent *e;
 	char **headers;
 	long long count = -2; // -2 for ../ and ./
 	long long i = 0;
 
 
 	// open our directory
-  dh = opendir(directory);
-  if(dh == NULL) {
-    fprintf(stderr, "could not open %s\n", directory);
-    exit(EXIT_FAILURE);
-  } 
+	dh = opendir(directory);
+	if(dh == NULL) {
+		fprintf(stderr, "could not open %s\n", directory);
+		exit(EXIT_FAILURE);
+	}
 
 	while((e = readdir(dh))) 
-		count++; 
-	
+		count++;
+
 	e = NULL;
 	rewinddir(dh);
 
@@ -61,7 +119,7 @@ char **get_fasta_files(char *directory) {
 	for(i = 0; i < count; i++) {
 		char *ext = NULL;
 		e = readdir(dh);
-			
+
 		if(strcmp(e->d_name, "..") == 0 || strcmp(e->d_name, ".") == 0) {
 			i--;
 			continue;
@@ -70,12 +128,13 @@ char **get_fasta_files(char *directory) {
 		ext = strrchr(e->d_name, '.');
 
 		if(str_eq(ext, ".fasta") || 
-			 str_eq(ext, ".fa") ||
-			 str_eq(ext, ".fna"))
+				str_eq(ext, ".fa") ||
+				str_eq(ext, ".fna"))
 		{
-			char *header = malloc(strlen(e->d_name) + 1);
+
+			char *header = malloc(strlen(directory) + strlen(e->d_name) + 1);
 			check_malloc(header, NULL);
-			strcpy(header, e->d_name);
+			sprintf(header, "%s/%s", directory, e->d_name); 
 			headers[array_pos] = header;
 		}
 		else {
@@ -90,151 +149,181 @@ char **get_fasta_files(char *directory) {
 	closedir(dh);
 	return headers;
 }
+
+
 int main(int argc, char **argv) {
 
-  int c;
+	int c;
 
-  char *input_fasta_directory = NULL;
-  char *sensing_matrix_filename = NULL;
-  char *output_filename = NULL;
+	char *input_fasta_directory = NULL;
+	char *input_fasta_filelist = NULL;
+	char *sensing_matrix_filename = NULL;
+	char *output_filename = NULL;
 
- 	unsigned long long i = 0;
- 	unsigned long long j = 0;
+	unsigned long long i = 0;
+	unsigned long long j = 0;
 
-  unsigned long long width = 0;
+	unsigned long long width = 0;
 
-  unsigned int kmer = 6;
-  unsigned long long lambda = 10000;
+	unsigned int kmer = 6;
+	unsigned long long lambda = 10000;
 
-  double rare_percent = 1.0;
+	double rare_percent = 1.0;
 
-  unsigned int jobs = 1;
+	unsigned int jobs = 1;
 	long done = 0;
 
 	unsigned long long dir_count = 0;
 
-  #ifdef Linux
-  jobs = get_nprocs();
-  #endif
-  #ifdef Darwin
-  jobs = sysconf (_SC_NPROCESSORS_ONLN);
-  #endif
-
-  int verbose = 0;
-
-  while (1) {
-    static struct option long_options[] = {
-      {"input-directory", required_argument, 0, 'i'},
-      {"kmer",  required_argument, 0, 'k'},
-      {"lambda",  required_argument, 0, 'l'},
-      {"jobs",  required_argument, 0, 'j'},
-      {"output", required_argument, 0, 'o'},
-      {"sensing-matrix", required_argument, 0, 's'},
-      {"rare-percent", required_argument, 0, 'r'},
-      {"verbose", no_argument, 0, 'v'},
-      {"help", no_argument, 0, 'h'},
-      {"version", no_argument, 0, 'V'},
-      {0, 0, 0, 0}
-    };
-    int option_index = 0;
-
-    c = getopt_long (argc, argv, "k:l:s:i:o:j:r:hvV", long_options, &option_index);
-
-    if (c == -1)
-      break;
-
-    switch (c) {
-      case 'i':
-        input_fasta_directory = optarg;
-        break;
-      case 'j':
-        jobs = atoi(optarg);
-        break;
-      case 'k':
-        kmer = atoi(optarg);
-        break;
-      case 'l':
-        lambda = atoi(optarg);
-        break;
-      case 'o':
-        output_filename = optarg;
-        break;
-      case 'r':
-        rare_percent = atof(optarg);
-        break;
-      case 's':
-        sensing_matrix_filename = optarg;
-        break;
-      case 'v':
-        verbose = 1;
-        break;
-      case 'V':
-        printf("%s\n", VERSION);
-        exit(EXIT_SUCCESS);
-        break;
-      case 'h':
-        puts(USAGE);
-        exit(EXIT_SUCCESS);
-        break;
-      default:
-        break;
-    }
-  }
+	#ifdef Linux
+		jobs = get_nprocs();
+	#endif
 
-  if(sensing_matrix_filename == NULL) {
-    fprintf(stderr, "Error: sensing matrix filename (-s) 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);
-    exit(EXIT_FAILURE);
-  }
-  if(input_fasta_directory == NULL) {
-    fprintf(stderr, "Error: input fasta directory (-i) must be specified\n\n");
-    fprintf(stderr, "%s\n", USAGE);
-    exit(EXIT_FAILURE);
-  }
+	#ifdef Darwin
+		jobs = sysconf (_SC_NPROCESSORS_ONLN);
+	#endif
+
+	int verbose = 0;
+
+	static struct option long_options[] = {
+		{"input-directory", required_argument, 0, 'i'},
+		{"input-filelist", required_argument, 0, 'f'},
+		{"kmer",  required_argument, 0, 'k'},
+		{"lambda",  required_argument, 0, 'l'},
+		{"jobs",  required_argument, 0, 'j'},
+		{"output", required_argument, 0, 'o'},
+		{"sensing-matrix", required_argument, 0, 's'},
+		{"rare-percent", required_argument, 0, 'r'},
+		{"verbose", no_argument, 0, 'v'},
+		{"help", no_argument, 0, 'h'},
+		{"version", no_argument, 0, 'V'},
+		{0, 0, 0, 0}
+	};
+
+	while (1) {
+		int option_index = 0;
+
+		c = getopt_long (argc, argv, "f:k:l:s:i:o:j:r:hvV", long_options, &option_index);
+
+		if (c == -1)
+			break;
+
+		switch (c) {
+			case 'i':
+				input_fasta_directory = optarg;
+				break;
+			case 'f':
+				input_fasta_filelist = optarg;
+				break;
+			case 'j':
+				jobs = atoi(optarg);
+				break;
+			case 'k':
+				kmer = atoi(optarg);
+				break;
+			case 'l':
+				lambda = atoi(optarg);
+				break;
+			case 'o':
+				output_filename = optarg;
+				break;
+			case 'r':
+				rare_percent = atof(optarg);
+				break;
+			case 's':
+				sensing_matrix_filename = optarg;
+				break;
+			case 'v':
+				verbose = 1;
+				break;
+			case 'V':
+				printf("%s\n", VERSION);
+				exit(EXIT_SUCCESS);
+				break;
+			case 'h':
+				puts(USAGE);
+				exit(EXIT_SUCCESS);
+				break;
+			default:
+				break;
+		}
+	}
+
+	if(sensing_matrix_filename == NULL) {
+		fprintf(stderr, "Error: sensing matrix filename (-s) 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);
+		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);
+		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);
+		exit(EXIT_FAILURE);
+	}
 
 	if(rare_percent <= 0 || rare_percent > 1.0) {
-    fprintf(stderr, "Error: rare percent must be between 0 and 1\n");
-    exit(EXIT_FAILURE);
+		fprintf(stderr, "Error: rare percent must be between 0 and 1\n");
+		exit(EXIT_FAILURE);
 	}
-  if(verbose) { 
-    printf("kmer: %u\n", kmer);
-    printf("lambda: %llu\n", lambda);
-    printf("input directory: %s\n", input_fasta_directory);
-    printf("sensing database: %s\n", sensing_matrix_filename);
-    printf("output: %s\n", output_filename);
-    printf("number of jobs to run at once: %d\n", jobs); 
-  }
 
-  if(access (sensing_matrix_filename, F_OK) == -1) {
-    fprintf(stderr, "Error: could not find %s\n", sensing_matrix_filename);
-    exit(EXIT_FAILURE);
-  }
+	if(verbose) { 
+		printf("kmer: %u\n", kmer);
+		printf("lambda: %llu\n", lambda);
+		printf("input directory: %s\n", input_fasta_directory);
+		printf("input filelist: %s\n", input_fasta_filelist);
+		printf("sensing database: %s\n", sensing_matrix_filename);
+		printf("output: %s\n", output_filename);
+		printf("number of jobs to run at once: %d\n", jobs); 
+	}
+
+	if(access (sensing_matrix_filename, F_OK) == -1) {
+		fprintf(stderr, "Error: could not find %s\n", sensing_matrix_filename);
+		exit(EXIT_FAILURE);
+	}
 
 	if(kmer == 0) {
-    fprintf(stderr, "Error: zero is not a valid kmer\n");
-    exit(EXIT_FAILURE);
+		fprintf(stderr, "Error: zero is not a valid kmer\n");
+		exit(EXIT_FAILURE);
 	}
 
-	char **filenames = get_fasta_files(input_fasta_directory);
+	// load filenames
+	char **filenames = NULL;
+	if(input_fasta_directory != NULL)
+		filenames = get_fasta_files_from_directory(input_fasta_directory);
+	else
+		filenames = get_fasta_files_from_file(input_fasta_filelist);
+
 	while(filenames[dir_count] != NULL)
 		dir_count++;
+	
+	if(dir_count == 0) {
+		fprintf(stderr, "Error: No files loaded from input\n");
+		exit(EXIT_FAILURE);
+	}
 
+	// 4 "ACGT" ^ Kmer gives us the size of output rows
+	width = pow(4, kmer);
 
-  // 4 "ACGT" ^ Kmer gives us the size of output rows
-  width = pow(4, kmer);
-
-  struct matrix *sensing_matrix = load_sensing_matrix(sensing_matrix_filename, kmer);
+	struct matrix *sensing_matrix = load_sensing_matrix(sensing_matrix_filename, kmer);
 	double *sensing_matrix_ptr = sensing_matrix->matrix;
 	unsigned long long sequences = sensing_matrix->sequences;
 
-  if(verbose) {
-    printf("directory count: %llu\n", dir_count);
-    printf("width: %llu\n", width);
+	if(verbose) {
+		printf("directory count: %llu\n", dir_count);
+		printf("width: %llu\n", width);
 		printf("sequences: %llu\n", sequences);
 	}
 
@@ -245,9 +334,12 @@ int main(int argc, char **argv) {
 	check_malloc(file_sequence_count, NULL);
 
 	#ifdef OMP
-  omp_set_num_threads(jobs);
+  	omp_set_num_threads(jobs);
 	#endif
+
+
   printf("Beginning to process samples\n"); 
+
   #pragma omp parallel for shared(solutions, sensing_matrix_ptr, width, done, sequences)
   for(size_t i = 0; i < dir_count; i++ ) {
 
@@ -261,12 +353,8 @@ int main(int argc, char **argv) {
 
 		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("processing %s\n", full_filename);
-		file_sequence_count = count_sequences(full_filename);
+		printf("processing %s\n", filenames[i]);
+		file_sequence_count = count_sequences(filenames[i]);
 
 		// load counts matrix
 		double *count_matrix = malloc(width * sizeof(double));
@@ -276,7 +364,7 @@ int main(int argc, char **argv) {
 
 		// convert our matrix into  doubles
 		{
-			unsigned long long *integer_counts = get_kmer_counts_from_file(full_filename, kmer);
+			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];
@@ -364,7 +452,6 @@ int main(int argc, char **argv) {
 		done++;
 		printf("%ld/%llu samples processed\n", done, dir_count); 
 		free(solution);
-		free(full_filename);
 		free(count_matrix_rare);
 		free(count_matrix);
 		free(sensing_matrix_rare);