reverse compliment

2 files changed, 108 insertions, 78 deletions

diff --git a/kmer_utils.c b/kmer_utils.c
index b8d5691..7703f0a 100644
--- a/kmer_utils.c
+++ b/kmer_utils.c
@@ -3,9 +3,10 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
+#include <stdbool.h>
 
 
-const unsigned char alpha[256] = 
+const unsigned char alpha[256] =
 {5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5,
@@ -19,6 +20,12 @@ const unsigned char alpha[256] =
 
 const char reverse_alpha[4] = { 'A', 'C', 'G', 'T' };
 
+													// compliments
+													// A  C  G  T  E  E
+													// T  G  C  A  E  E
+const char compliment[6] = { 3, 2, 1, 0, 5, 5};
+
+
 unsigned long long pow_four(unsigned long long x) {
 	return (unsigned long long)1 << (x * 2);
 }
@@ -27,14 +34,53 @@ void check_null_ptr(void *ptr, const char *error) {
 	if (ptr == NULL) {
 		if(error != NULL)  {
 			fprintf(stderr, "Error: %s - %s\n", error, strerror(errno));
-		} 
+		}
 		else {
 			fprintf(stderr, "Error: %s\n", strerror(errno));
-		} 
+		}
 		exit(EXIT_FAILURE);
 	}
 }
 
+
+void reverse_string(char *s, size_t len) {
+	char t, *d = &(s[len - 1]);
+	while (d > s) {
+		t = *s;
+		*s++ = *d;
+		*d-- = t;
+	}
+}
+
+void count_sequence(const char *seq, const size_t seq_length, const unsigned int kmer, unsigned long long *counts) {
+	long long position;
+	long long i;
+
+	// loop through our seq to process each k-mer
+	for(position = 0; position < (signed)(seq_length - kmer + 1); position++) {
+		unsigned long long mer = 0;
+		unsigned long long multiply = 1;
+
+		// for each char in the k-mer check if it is an error char
+		for(i = position + kmer - 1; i >= position; i--){
+			if(seq[i] == 5) {
+				position = i;
+				goto next;
+			}
+
+			// multiply this char in the mer by the multiply
+			// and bitshift the multiply for the next round
+			mer += seq[i] * multiply;
+			multiply = multiply << 2;
+		}
+		// bump up the mer value in the counts array
+		counts[mer]++;
+
+		// skip count if error
+		next: ;
+	}
+}
+
 // convert a string of k-mer size base-4 values  into a
 // base-10 index
 unsigned long num_to_index(const char *str, const int kmer, const long error_pos, long long *current_position) {
@@ -44,7 +90,7 @@ unsigned long num_to_index(const char *str, const int kmer, const long error_pos
 	unsigned long multiply = 1;
 
 	for(i = kmer - 1; i >= 0; i--){
-		if(str[i] == 5) { 
+		if(str[i] == 5) {
 			current_position += i;
 			return error_pos;
 		}
@@ -57,7 +103,7 @@ unsigned long num_to_index(const char *str, const int kmer, const long error_pos
 }
 
 // return the number of loaded elements
-unsigned long long load_specific_mers_from_file(char *fn, unsigned int kmer, size_t width, size_t *arr) { 
+unsigned long long load_specific_mers_from_file(char *fn, unsigned int kmer, size_t width, size_t *arr) {
 		FILE *fh;
 		size_t arr_pos = 0;
 		char line[64];
@@ -130,11 +176,11 @@ char *index_to_kmer(unsigned long long index, long kmer)  {
 	size_t start = i ;
 
 	// decrement i by 1 to reverse the last i++
-	i--;  
+	i--;
 	j = 0;
 
 	// reverse the array, as j increases, decrease i
-	for(j = 0; j < start; j++, i--) 
+	for(j = 0; j < start; j++, i--)
 		ret[j + offset] = reverse_alpha[(int)num_array[i]];
 	
   // set our last character to the null termination byte
@@ -165,7 +211,7 @@ size_t strnstrip(char *s, int c, size_t len) {
 
 }
 
-unsigned long long * get_kmer_counts_from_file(FILE *fh, const unsigned int kmer) {
+unsigned long long * get_kmer_counts_from_file(FILE *fh, const unsigned int kmer, const bool count_compliment) {
 	
 	char *line = NULL;
 	size_t len = 0;
@@ -184,9 +230,6 @@ unsigned long long * get_kmer_counts_from_file(FILE *fh, const unsigned int kmer
 		char *seq;
 		size_t seq_length;
 
-		long long i = 0;
-		long long position = 0;
-
 		// find our first \n, this should be the end of the header
 		seq = strchr(line, '\n');	
 		if(seq == NULL) 
@@ -204,31 +247,18 @@ unsigned long long * get_kmer_counts_from_file(FILE *fh, const unsigned int kmer
 		for(k = 0; k < seq_length; k++)
 			seq[k] = alpha[(int)seq[k]];
 		
+		count_sequence(seq, seq_length, kmer, counts);
 
-		// loop through our seq to process each k-mer
-		for(position = 0; position < (signed)(seq_length - kmer + 1); position++) {
-			unsigned long long mer = 0;
-			unsigned long long multiply = 1;
-
-			// for each char in the k-mer check if it is an error char
-			for(i = position + kmer - 1; i >= position; i--){
-				if(seq[i] == 5) { 
-					mer = width;
-					position = i;
-					goto next;
-				}
-
-				// multiply this char in the mer by the multiply
-				// and bitshift the multiply for the next round
-				mer += seq[i] * multiply;
-				multiply = multiply << 2;
+		if(count_compliment) {
+			for(k = 0; k < seq_length; k++) { 
+				seq[k] = compliment[(int)seq[k]];
 			}
-			// use this point to get mer of our loop
-			next:
-			// bump up the mer value in the counts array
-			counts[mer]++;
+			
+			reverse_string(seq, seq_length);
+			count_sequence(seq, seq_length, kmer, counts);
+			
 		}
-	} 
+	}
 
 
   free(line);
@@ -237,15 +267,14 @@ unsigned long long * get_kmer_counts_from_file(FILE *fh, const unsigned int kmer
 	return counts;
 }
 
-unsigned long long * get_kmer_counts_from_filename(const char *fn, const unsigned int kmer) {
+unsigned long long * get_kmer_counts_from_filename(const char *fn, const unsigned int kmer, const bool count_compliment) {
 		FILE *fh = fopen(fn, "r");
 		check_null_ptr(fh, fn);
 
-		return get_kmer_counts_from_file(fh, kmer);
+		return get_kmer_counts_from_file(fh, kmer, count_compliment);
 }
 
-
-unsigned long long * get_continuous_kmer_counts_from_file(FILE *fh, const unsigned int kmer) {
+unsigned long long * get_continuous_kmer_counts_from_file(FILE *fh, const unsigned int kmer, const bool count_compliment) {
 	
 	char *line = NULL;
 	size_t len = 0;
@@ -262,13 +291,9 @@ unsigned long long * get_continuous_kmer_counts_from_file(FILE *fh, const unsign
 	size_t cpy_size = kmer - 1;
 
 	char *end_of_previous = malloc(sizeof(char) * cpy_size);
+	check_null_ptr(end_of_previous, NULL);
 	memset(end_of_previous, 5, cpy_size);
 
-	if(end_of_previous == NULL) {
-		fprintf(stderr, "%s\n", strerror(errno));
-		exit(EXIT_FAILURE);
-	}
-
 	while ((read = getline(&line, &len, fh)) != -1) {
 		if(line[0] == '>')
 			continue;
@@ -276,7 +301,6 @@ unsigned long long * get_continuous_kmer_counts_from_file(FILE *fh, const unsign
 		char *seq;
 		size_t j;
 		size_t k;
-		long long position;
 		size_t seq_length;
 
 		seq = malloc(read + cpy_size);
@@ -290,40 +314,23 @@ unsigned long long * get_continuous_kmer_counts_from_file(FILE *fh, const unsign
 		// everything else is 5 
 		for(k = cpy_size; k < seq_length; k++)
 			seq[k] = alpha[(int)seq[k]];
-		
 
-		// loop through our seq to process each k-mer
-		for(position = 0; position < (signed)(seq_length - kmer + 1); position++) {
-			unsigned long long mer = 0;
-			unsigned long long multiply = 1;
-			long long i;
-
-			// for each char in the k-mer check if it is an error char
-			for(i = position + kmer - 1; i >= position; i--){
-				if(seq[i] == 5) { 
-					mer = width;
-					position = i;
-					goto next;
-				}
-
-				// multiply this char in the mer by the multiply
-				// and bitshift the multiply for the next round
-				mer += seq[i] * multiply;
-				multiply = multiply << 2;
-			}
-			// use this point to get mer of our loop
-			next:
-			// bump up the mer value in the counts array
-			counts[mer]++;
-		}
+		count_sequence(seq, seq_length, kmer, counts);
 
 		for(j = 0, k = seq_length - (cpy_size + 1); k < seq_length; k++, j++) {
 			end_of_previous[j] = seq[k];
 		}
 
-		free(seq);
+		if(count_compliment) {
+			for(k = 0; k < seq_length; k++) 
+				seq[k] = compliment[(int)seq[k]];
 
-	} 
+			reverse_string(seq, seq_length);
+			count_sequence(seq, seq_length, kmer, counts);
+		}
+
+				free(seq);
+	}
 
 	free(end_of_previous);
   free(line);
@@ -332,9 +339,9 @@ unsigned long long * get_continuous_kmer_counts_from_file(FILE *fh, const unsign
 	return counts;
 }
 
-unsigned long long * get_continuous_kmer_counts_from_filename(const char *fn, const unsigned int kmer) {
+unsigned long long * get_continuous_kmer_counts_from_filename(const char *fn, const unsigned int kmer, const bool count_compliment) {
 		FILE *fh = fopen(fn, "r");
 		check_null_ptr(fh, fn);
 
-		return get_continuous_kmer_counts_from_file(fh, kmer);
+		return get_continuous_kmer_counts_from_file(fh, kmer, count_compliment);
 }
diff --git a/kmer_utils.h b/kmer_utils.h
index 4bc732a..a727da8 100644
--- a/kmer_utils.h
+++ b/kmer_utils.h
@@ -1,22 +1,45 @@
-// Kmer functions
-void convert_kmer_to_num(char *str, const unsigned long length);
+// dna-util's function library.
+
 unsigned long num_to_index(const char *str, const int kmer, const long error_pos, long long *current_position);
 char *index_to_kmer(unsigned long long index, long kmer);
 
 // Utility functions
+
+
+// strip char 'c' out of char array *s of length len
 size_t strnstrip(char *s, int c, size_t len);
+
+// reverse char arry *s of length len
+void reverse_string(char *s, size_t len);
+
+// quicky calculate 4^x 
 unsigned long long pow_four(unsigned long long x);
+
+// check if pointer is null. a helper for dealing with NULL
+// return values as errors. Calls strerror and quits if 
+// ptr is null, optionally takes *error char array as 
+// a error to output
 void check_null_ptr(void *ptr, const char *error);
 
+void count_sequence(const char *seq, const size_t seq_length, const unsigned int kmer, unsigned long long *counts);
+
 // Variables
+//
 const unsigned char alpha[256]; 
+const unsigned char reverse_alpha[4];
+const unsigned char compliment[5];
+
 
 // file loading functions
+
+// open file from filename in char array *fn, and try and parse in one mer per
+// line, of size kmer, and store the indicies of those mers in the *arr
+// pointer;
 unsigned long long load_specific_mers_from_file(const char *fn, unsigned int kmer, size_t width, size_t *arr);
 
-unsigned long long * get_kmer_counts_from_filename(const char *fn, const unsigned int kmer);
-unsigned long long * get_kmer_counts_from_file(FILE *fh, const int kmer);
+unsigned long long * get_kmer_counts_from_filename(const char *fn, const unsigned int kmer, const bool count_compliment);
+unsigned long long * get_kmer_counts_from_file(FILE *fh, const int kmer, const bool count_compliment);
 
-unsigned long long * get_continuous_kmer_counts_from_filename(const char *fn, const unsigned int kmer);
-unsigned long long * get_continuous_kmer_counts_from_file(FILE *fh, const unsigned int kmer);
+unsigned long long * get_continuous_kmer_counts_from_filename(const char *fn, const unsigned int kmer, const bool count_compliment);
+unsigned long long * get_continuous_kmer_counts_from_file(FILE *fh, const unsigned int kmer, const bool count_compliment);