add kmer_continuous_count

this tool will count continuously, instead of line by line. The way that
this works out is something like this:

test.fa
> header 1
AAAAATTTTT
> header 2
GGGGGAAAAA

counting 6 mers, the program will count TTTGGG,  TTGGGG, TGGGGG, like
there was no header seperating them. This can be useful for certain
tyeps of processing, like when the sequences are continuous from a
genome.

initial commit

4 files changed, 268 insertions, 2 deletions

diff --git a/Makefile b/Makefile
index c929cfd..dc47796 100644
--- a/Makefile
+++ b/Makefile
@@ -4,7 +4,7 @@ CFLAGS = -O3 -s -mtune=native -Wall -DVERSION=$(VERSION) -Wextra
 DESTDIR = /usr/local/
 
 
-all: libkmer.o libkmer.so kmer_total_count kmer_counts_per_sequence
+all: libkmer.o libkmer.so kmer_total_count kmer_counts_per_sequence kmer_continuous_count
 
 libkmer.o: kmer_utils.c
 	$(CC) -c kmer_utils.c -o libkmer.o $(CFLAGS) -fPIC
@@ -14,9 +14,11 @@ kmer_total_count: libkmer.o kmer_total_count.c kmer_utils.h
 	$(CC) libkmer.o kmer_total_count.c -o kmer_total_count $(CLIBS) $(CFLAGS)
 kmer_counts_per_sequence: libkmer.o kmer_counts_per_sequence.c kmer_utils.h
 	$(CC) libkmer.o kmer_counts_per_sequence.c -o kmer_counts_per_sequence $(CLIBS) $(CFLAGS)
+kmer_continuous_count: libkmer.o kmer_continuous_count.c kmer_utils.h
+	$(CC) libkmer.o kmer_continuous_count.c -o kmer_continuous_count $(CLIBS) $(CFLAGS)
 
 clean:
-	rm -vf kmer_total_count kmer_counts_per_sequence libkmer.so libkmer.o
+	rm -vf kmer_total_count kmer_counts_per_sequence kmer_continuous_count libkmer.so libkmer.o
 
 debug: CFLAGS = -ggdb -Wall -Wextra -DVERSION=$(VERSION)\"-debug\"
 debug: all
diff --git a/kmer_continuous_count.c b/kmer_continuous_count.c
new file mode 100644
index 0000000..5ace9a5
--- /dev/null
+++ b/kmer_continuous_count.c
@@ -0,0 +1,158 @@
+
+// Copyright 2013 Calvin Morrison
+#include <errno.h>
+#include <stdbool.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <getopt.h>
+
+#include "kmer_utils.h"
+
+
+void help() {
+	printf("usage: kmer_total_count -i input_file -k kmer [-n] [-l] ...\n\n"
+				 "count mers in size k from a fasta file, but do so continuously\n"
+				 "\n"
+				 "  --input    -i  input fasta file to count\n"
+				 "  --kmer     -k  size of mers to count\n"
+				 "  --nonzero  -n  only print non-zero values\n"
+				 "  --label    -l  print mer along with value\n"
+				 "\n"
+				 "Report all bugs to mutantturkey@gmail.com\n"
+				 "\n"
+				 "Copyright 2014 Calvin Morrison, Drexel University.\n"
+				 "\n"
+				 "If you are using any dna-utils tool for a publication\n"
+				 "please cite your usage:\n\n"
+				 "dna-utils. Drexel University, Philadelphia USA, 2014;\n"
+				 "software available at www.github.com/EESI/dna-utils/\n");
+}
+
+
+int main(int argc, char **argv) {
+
+	char *fn = NULL;
+	FILE *fh = NULL;
+
+	unsigned int kmer = 0;
+
+	bool nonzero = false;
+	bool label = false;
+	bool kmer_set = false;
+
+	unsigned long long width = 0;
+
+	unsigned long long i = 0;
+
+	static struct option long_options[] = {
+		{"input", required_argument, 0, 'i'},
+		{"kmer",  required_argument, 0, 'k'},
+		{"nonzero", no_argument, 0, 'n'},
+		{"label", no_argument, 0, 'l'},
+		{"help", no_argument, 0, 'h'},
+		{0, 0, 0, 0}
+	};
+
+	while (1) {
+
+		int option_index = 0;
+		int c = 0;
+
+		c = getopt_long (argc, argv, "i:k:nlvh", long_options, &option_index);
+
+		if (c == -1)
+			break;
+
+		switch (c) {
+			case 'i':
+				fn = optarg;
+				break;
+			case 'k':
+				kmer = atoi(optarg);
+				kmer_set = true;
+				break;
+			case 'n':
+				nonzero = true; 
+				break;
+			case 'l':
+				label = true;
+				break;
+			case 'h':
+				help();
+				exit(EXIT_SUCCESS);
+				break;
+			case 'v':
+				printf("dna-utils version " VERSION "\n");
+				exit(EXIT_SUCCESS);
+				break;
+			default:
+				break;
+		}
+	}
+	if(argc == 1) {
+		help();
+		exit(EXIT_FAILURE);
+	}
+	if(fn == NULL) {
+		fprintf(stderr, "no input file specified with -i, reading from stdin\n");
+		fh = stdin;
+	}
+	else {
+		fh = fopen(fn, "r");
+		if(fh == NULL) {
+			fprintf(stderr, "Could not open %s - %s\n", fn, strerror(errno));
+			exit(EXIT_FAILURE);
+		}
+	}
+	if(!kmer_set) {
+		fprintf(stderr, "Error: kmer (-k) must be supplied\n");
+		exit(EXIT_FAILURE);
+	}
+	if(kmer == 0) { 
+		fprintf(stderr, "Error: invalid kmer - '%d'.\n", kmer);
+		exit(EXIT_FAILURE);
+	}
+
+	width = pow_four(kmer);
+
+	unsigned long long *counts = get_continuous_kmer_counts_from_file(fh, kmer);
+
+	// If nonzero is set, only print non zeros
+	if(nonzero) {
+		// if labels is set, print out our labels
+		if(label) {
+			for(i = 0; i < width; i++)
+				if(counts[i] != 0) {
+					char *kmer_str = index_to_kmer(i, kmer);
+					fprintf(stdout, "%s\t%llu\n", kmer_str, counts[i]);
+					free(kmer_str);
+				}
+
+		}
+		else {
+			for(i = 0; i < width; i++)
+				if(counts[i] != 0) 
+					fprintf(stdout, "%llu\t%llu\n", i, counts[i]);
+
+		}
+	}
+	// If we aren't printing nonzeros print everything
+	else {
+		if(label) {
+			for(i = 0; i < width; i++) {
+				char *kmer_str = index_to_kmer(i, kmer);
+				fprintf(stdout, "%s\t%llu\n", kmer_str, counts[i]);
+				free(kmer_str);
+			} 
+		}
+		else {
+			for(i = 0; i < width; i=i+4) {
+				fprintf(stdout, "%llu\n%llu\n%llu\n%llu\n", counts[i], counts[i+1], counts[i+2], counts[i+3]);
+			}
+		}
+	}
+
+	free(counts);
+	return EXIT_SUCCESS;
+}
diff --git a/kmer_utils.c b/kmer_utils.c
index 81b1e91..79c9180 100644
--- a/kmer_utils.c
+++ b/kmer_utils.c
@@ -226,6 +226,7 @@ unsigned long long * get_kmer_counts_from_file(FILE *fh, const unsigned int kmer
 		}
 	} 
 
+
   free(line);
 	fclose(fh);
 
@@ -242,3 +243,104 @@ unsigned long long * get_kmer_counts_from_filename(const char *fn, const unsigne
 		return get_kmer_counts_from_file(fh, kmer);
 }
 
+
+unsigned long long * get_continuous_kmer_counts_from_file(FILE *fh, const unsigned int kmer) {
+	
+	char *line = NULL;
+	size_t len = 0;
+	ssize_t read;
+
+	// width is 4^kmer  
+	// there's a sneaky bitshift to avoid pow dependency
+	const unsigned long width = pow_four(kmer); 
+
+	// malloc our return array
+	unsigned long long * counts = calloc((width+ 1), sizeof(unsigned long long));
+	if(counts == NULL)  {
+		fprintf(stderr, "%s\n", strerror(errno));
+		exit(EXIT_FAILURE);
+	}
+
+	size_t cpy_size = kmer - 1;
+
+	char *end_of_previous = malloc(sizeof(char) * cpy_size);
+	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;
+
+		char *seq;
+		size_t j;
+		size_t k;
+		long long position;
+		size_t seq_length;
+
+		seq = malloc(read + cpy_size);
+
+		memcpy(seq, end_of_previous, cpy_size);
+		memcpy(seq + cpy_size, line, read);
+
+		seq_length = read + cpy_size;
+
+		// relace A, C, G and T with 0, 1, 2, 3 respectively
+		// 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]++;
+		}
+
+		for(j = 0, k = seq_length - (cpy_size + 1); k < seq_length; k++, j++) {
+			end_of_previous[j] = seq[k];
+		}
+
+		free(seq);
+
+	} 
+
+
+	free(end_of_previous);
+  free(line);
+	fclose(fh);
+
+	return counts;
+}
+
+unsigned long long * get_continuous_kmer_counts_from_filename(const char *fn, const unsigned int kmer) {
+		FILE *fh = fopen(fn, "r");
+		if(fh == NULL) {
+			fprintf(stderr, "Could not open %s - %s\n", fn, strerror(errno));
+			return NULL;
+		}
+
+		return get_continuous_kmer_counts_from_file(fh, kmer);
+}
diff --git a/kmer_utils.h b/kmer_utils.h
index ceb28eb..ae48136 100644
--- a/kmer_utils.h
+++ b/kmer_utils.h
@@ -12,5 +12,9 @@ const unsigned char alpha[256];
 
 // file loading functions
 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_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);