1 files changed, 58 insertions, 0 deletions
diff --git a/kmer_frequency_per_sequence.c b/kmer_frequency_per_sequence.c
new file mode 100644
index 0000000..e0995f9
--- /dev/null
+++ b/kmer_frequency_per_sequence.c
@@ -0,0 +1,58 @@
+// Copyright 2013 Calvin Morrison
+#include <stdio.h>
+#include <math.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <stdint.h>
+
+#include "kmer_utils.h"
+
+int main(int argc, char **argv) {
+
+  char *line = NULL;
+  long kmer = 6;
+  size_t len = 0;
+  ssize_t read;
+
+  if(argc != 3) {
+    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);
+  }
+
+
+  int width = (int)pow(4, kmer);
+  while ((read = getline(&line, &len, fh)) != -1) {
+    if(line[0] != '>')   {
+
+      unsigned long long *counts = malloc((width+ 1) * sizeof(unsigned long long));
+      if(counts == NULL) 
+        exit(EXIT_FAILURE);
+
+      unsigned int i = 0;
+      for(i = 0; i < strlen(line) - kmer; i++) {
+        counts[convert_kmer_to_index(&line[i], kmer, width)]++;
+      }
+
+      unsigned long total = 0;
+      for(i = 0; i < width; i++)
+        total += counts[i];
+
+      for(i = 0; i < width - 1; i++)
+        printf("%.12f\t", (double)counts[i] / total);
+      printf("%.12f\n", (double)counts[width - 1] / total);
+
+      free(counts);
+    }
+  }
+
+  free(line);
+
+
+  return EXIT_SUCCESS;
+}