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-rwxr-xr-xcount_nucleobasesbin5496 -> 0 bytes
-rwxr-xr-xcount_nucleobases.c53
2 files changed, 27 insertions, 26 deletions
diff --git a/count_nucleobases b/count_nucleobases
deleted file mode 100755
index 8c1b122..0000000
--- a/count_nucleobases
+++ /dev/null
Binary files differ
diff --git a/count_nucleobases.c b/count_nucleobases.c
index c2aafe5..4bc3ca1 100755
--- a/count_nucleobases.c
+++ b/count_nucleobases.c
@@ -3,35 +3,36 @@
#include <stdlib.h>
#include <unistd.h>
#include <stdint.h>
-int main(int argc, char **argv) {
+#include <stdbool.h>
+int main() {
- char *line = NULL;
- size_t len = 0;
- ssize_t read;
-
- if(argc != 2) {
- printf("Please supply a filename, and only a filename\n");
- exit(EXIT_FAILURE);
- }
-
- FILE *fh = fopen(argv[1], "r" );
- if(fh == NULL) {
- fprintf(stderr, "Couldn't open: %s\n", argv[1]);
- exit(EXIT_FAILURE);
- }
+ ssize_t len = 0;
unsigned long long counts[256] = {0};
-
- while ((read = getline(&line, &len, fh)) != -1) {
- if(line[0] != '>') {
- unsigned int i = 0;
- for(i = 0; i < strlen(line); i++) {
- counts[line[i]]++;
- }
- }
- }
-
- free(line);
+ char buffer[4096];
+ bool header = false;
+
+ len = fread(&buffer, 1, 1, stdin);
+
+ if(len != NULL) {
+ if(buffer[0] == '>') {
+ header = true;
+ while((len = fread(&buffer, 1, 4096, stdin)) != NULL) {
+ unsigned int i = 0;
+ for(i = 0; i < len; i++) {
+ if(buffer[i] == '>') {
+ header = true;
+ continue;
+ }
+ else if(buffer[i] == '\n' && header == true)
+ header = false;
+ if(header == false ) {
+ counts[(int)buffer[i]]++;
+ }
+ }
+ }
+ } else { fprintf(stderr, "this does not look like a fasta file\n"); }
+ } else { fprintf(stderr, "could not read file\n"); }
printf("A:%llu\nC:%llu\nG:%llu\nT:%llu\n",
counts['a'] + counts['A'],