add sequence length command

1 files changed, 55 insertions, 0 deletions

diff --git a/src/sequence_length.c b/src/sequence_length.c
new file mode 100644
index 0000000..b31aac3
--- /dev/null
+++ b/src/sequence_length.c
@@ -0,0 +1,55 @@
+// Copyright 2013 Calvin Morrison
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <stdint.h>
+#include <stdbool.h>
+#include <errno.h>
+int main() {
+
+	ssize_t len = 0;
+
+	char buffer[4096];
+	bool header = false;
+
+	len = fread(&buffer, 1, 1, stdin);
+
+	unsigned long long seq_length = 0;
+	if(!errno) {
+		if(buffer[0] == '>') {
+			header = true;
+
+			while((len = fread(&buffer, 1, 4096, stdin)) != 0) {
+				size_t i = 0;                                                                    
+				for(i = 0; i < len; i++) {
+					if(buffer[i] == '>') {
+						printf("%llu\n", seq_length);
+						seq_length = 0;
+						header = true;
+						continue;
+					}   
+					else if(buffer[i] == '\n' && header == true) {
+						header = false;
+						continue;
+					}
+					if(header == false && buffer[i] != '\n') { 
+						seq_length++;
+					}   
+				}   
+			}   
+		} 
+		else { 
+			fprintf(stderr, "this does not look like a fasta file\n"); 
+			return EXIT_FAILURE;
+		}
+	} 
+	else { 
+		fprintf(stderr, "could not read file\n"); 
+		return EXIT_FAILURE;
+	}
+
+	printf("%llu\n", seq_length);
+
+	return EXIT_SUCCESS;
+}
+