From b508436d6982205508d531ba19c9980570946ae7 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Thu, 7 Nov 2013 17:25:06 -0500 Subject: rename to counts per sequence, don't provide frequencies only counts --- kmer_frequency_per_sequence.c | 71 ------------------------------------------- 1 file changed, 71 deletions(-) delete mode 100644 kmer_frequency_per_sequence.c (limited to 'kmer_frequency_per_sequence.c') diff --git a/kmer_frequency_per_sequence.c b/kmer_frequency_per_sequence.c deleted file mode 100644 index 7b14f6d..0000000 --- a/kmer_frequency_per_sequence.c +++ /dev/null @@ -1,71 +0,0 @@ -// Copyright 2013 Calvin Morrison -#include -#include -#include -#include - -#include "kmer_utils.h" - -unsigned long position = 0; -int main(int argc, char **argv) { - - char *line = NULL; - size_t len = 0; - ssize_t read; - - if(argc != 3) { - printf("Please supply a filename and a kmer\n"); - exit(EXIT_FAILURE); - } - - FILE *fh = fopen(argv[1], "r" ); - if(fh == NULL) { - fprintf(stderr, "Error opening %s - %s\n", argv[1], strerror(errno)); - exit(EXIT_FAILURE); - } - - unsigned long kmer = atoi(argv[2]); - if(kmer == 0) { - fprintf(stderr, "Error: invalid kmer.\n"); - exit(EXIT_FAILURE); - } - - const unsigned long width = (unsigned long)1 << (kmer * 2); - - 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] != '>' && (read > kmer)) { - - unsigned int i = 0; - unsigned long total = 0; - - // reset our count matrix to zero - memset(counts, 0, width * sizeof(unsigned long long)); - - for(i = 0; i < read - kmer; i++) { - line[i] = alpha[(int)line[i]]; - } - - for(i = 0; i < read - kmer; i++) { - counts[num_to_index(&line[i],kmer, width)]++; - } - - 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; -} -- cgit v1.2.3