Initial commit of some kmer utilities.

there are two utilties included.

one is kmer_frequency_per_sequence,
which outputs a (m x n) matrix where m is the sequence, and n is the
frequency of that nmer to occur in the given sequence.

the other tool is kmer_total_count, which counts kmers for the total
file, not just one sequence

5 files changed, 175 insertions, 0 deletions

diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..df96037
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,13 @@
+VERSION=\"v0.0.1\"
+CC = gcc
+CFLAGS = -O3 -s -mtune=native -Wall -lm -DVERSION=$(VERSION)
+
+all: kmer_total_count kmer_frequency_per_sequence
+
+kmer_total_count:
+	$(CC) kmer_total_count.c kmer_utils.c -o kmer_count_total $(CFLAGS)
+kmer_frequency_per_sequence:
+	$(CC) kmer_frequency_per_sequence.c kmer_utils.c -o kmer_frequency_per_sequence $(CFLAGS)
+
+clean:
+	rm -vf kmer_total_count kmer_frequency_per_sequence
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;
+}
diff --git a/kmer_total_count.c b/kmer_total_count.c
new file mode 100644
index 0000000..4d1ab87
--- /dev/null
+++ b/kmer_total_count.c
@@ -0,0 +1,49 @@
+// 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;
+  size_t len = 0;
+  ssize_t read;
+  unsigned int i = 0;
+
+  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 kmer = atoi(argv[2]);
+  int width = (int)pow(4, kmer);
+
+  unsigned long long *counts = malloc((width+ 1) * sizeof(unsigned long long));
+  if(counts == NULL) 
+    exit(EXIT_FAILURE);
+
+  while ((read = getline(&line, &len, fh)) != -1) {
+    if(line[0] != '>')   {
+
+      for(i = 0; i < strlen(line) - kmer; i++) {
+        counts[convert_kmer_to_index(&line[i],kmer, width)]++;
+      }
+    }
+  }
+
+  for(i = 0; i < width; i++)
+    printf("%llu\n", counts[i]);
+
+
+  return EXIT_SUCCESS;
+}
diff --git a/kmer_utils.c b/kmer_utils.c
new file mode 100644
index 0000000..b6f66b5
--- /dev/null
+++ b/kmer_utils.c
@@ -0,0 +1,54 @@
+#include <stdint.h>
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+
+// This function takes a char array containing sequences and converts it
+// into a kmer index (essentially a base 4 radix converstion to base 10, with
+// some mumbo-jumbo of taking each of the characters we want (ACGT) and turning
+// them into a radix-4 number we can use.
+//
+// kind of convoluted but it works.
+//
+// Arguemnts: 
+//  char *str - a NULL terminated character array 
+//  long kmer - how long of a index value you want to return
+//  long error_pos - what index to return for a non ACGT character
+//
+long convert_kmer_to_index(char *str, long kmer, long error_pos) {
+
+  char **ptr = NULL;
+  char vals[kmer];
+  long i = 0;
+  long ret = 0;
+
+  for(i = 0; i < kmer; i++) {
+    int val = 0;
+    switch(str[i]) {
+      case 'a':
+      case 'A':
+        val = 48;
+        break;
+      case 'c':
+      case 'C':
+        val = 49;
+        break;
+      case 'g':
+      case 'G':
+        val = 50;
+        break;
+      case 't':
+      case 'T':
+        val = 51;
+        break;
+      default:
+        return error_pos; 
+    }
+
+
+    vals[i] = val; 
+  }
+
+  ret = strtol(vals, ptr, 4);
+  return ret;
+}
diff --git a/kmer_utils.h b/kmer_utils.h
new file mode 100644
index 0000000..a93216e
--- /dev/null
+++ b/kmer_utils.h
@@ -0,0 +1 @@
+long convert_kmer_to_index(char *str, long kmer, long error_pos);