From 5f73d9a17280b0a388936365bace8a64a5568cea Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Tue, 29 Oct 2013 16:27:38 -0400
Subject: remove the fasta file requirement for multifasta, and no longer parse
headers (we already do)
---
src/c/multifasta_to_otu.c | 22 ++--------------------
1 file changed, 2 insertions(+), 20 deletions(-)
(limited to 'src')
diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c
index d4d1588..72d13b5 100644
--- a/src/c/multifasta_to_otu.c
+++ b/src/c/multifasta_to_otu.c
@@ -28,7 +28,6 @@ int main(int argc, char **argv) {
char *input_fasta_directory = NULL;
char *sensing_matrix_filename = NULL;
- char *sensing_fasta_filename = NULL;
char *output_filename = NULL;
unsigned long long x = 0;
@@ -63,7 +62,6 @@ int main(int argc, char **argv) {
{"lambda", required_argument, 0, 'l'},
{"jobs", required_argument, 0, 'j'},
{"output", required_argument, 0, 'o'},
- {"sensing-fasta", required_argument, 0, 'f'},
{"sensing-matrix", required_argument, 0, 's'},
{"verbose", no_argument, 0, 'v'},
{"help", no_argument, 0, 'h'},
@@ -72,7 +70,7 @@ int main(int argc, char **argv) {
};
int option_index = 0;
- c = getopt_long (argc, argv, "k:l:f:s:i:o:j:hvV", long_options, &option_index);
+ c = getopt_long (argc, argv, "k:l:s:i:o:j:hvV", long_options, &option_index);
if (c == -1)
break;
@@ -84,9 +82,6 @@ int main(int argc, char **argv) {
case 'l':
lambda = atoi(optarg);
break;
- case 'f':
- sensing_fasta_filename = optarg;
- break;
case 's':
sensing_matrix_filename = optarg;
break;
@@ -120,11 +115,6 @@ int main(int argc, char **argv) {
fprintf(stderr, "%s\n", USAGE);
exit(EXIT_FAILURE);
}
- if(sensing_fasta_filename == NULL) {
- fprintf(stderr, "Error: sensing fasta filename (-f) 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);
@@ -141,7 +131,6 @@ int main(int argc, char **argv) {
printf("lambda: %llu\n", lambda);
printf("input directory: %s\n", input_fasta_directory);
printf("sensing database: %s\n", sensing_matrix_filename);
- printf("sensing database fasta: %s\n", sensing_fasta_filename);
printf("output: %s\n", output_filename);
printf("number of jobs to run at once: %d\n", jobs);
}
@@ -152,11 +141,6 @@ int main(int argc, char **argv) {
exit(EXIT_FAILURE);
}
- if(access (sensing_fasta_filename, F_OK) == -1) {
- fprintf(stderr, "Error: could not find %s\n", sensing_fasta_filename);
- exit(EXIT_FAILURE);
- }
-
input_directory_dh = opendir(input_fasta_directory);
if(input_directory_dh == NULL) {
fprintf(stderr, "could not open %s\n", input_fasta_directory);
@@ -303,8 +287,6 @@ int main(int argc, char **argv) {
free(sensing_matrix_copy);
}
- char **headers = load_headers(sensing_fasta_filename, sensing_matrix->sequences);
-
// output our matrix
FILE *output_fh = fopen(output_filename, "w");
if(output_fh == NULL) {
@@ -337,7 +319,7 @@ int main(int argc, char **argv) {
// if our column is zero, don't bother printing the row
if(column_sum != 0) {
- fprintf(output_fh, "%s\t", headers[y]);
+ fprintf(output_fh, "%s\t", sensing_matrix->headers[y]);
for(i = 0; i < dir_count - 1; i++) {
fprintf(output_fh, "%d\t", (int)solutions[sensing_matrix->sequences*i + y]);
--
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