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

1 files changed, 158 insertions, 0 deletions

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;
+}