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sequence.c
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sequence.c
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/******************************************************************************\
sequence.c
Copyright (C) Ian Korf
\******************************************************************************/
#ifndef GENOMIKON_SEQUENCE_C
#define GENOMIKON_SEQUENCE_C
#include "sequence.h"
// Utilities
int gkn_mem2idx(const char *seq, int off, int len) {
int idx = 0;
for (int i = 0; i < len; i++) {
switch (seq[off+i]) {
case 'A': case 'a': idx += pow(4, (len -i -1)) * 0; break;
case 'C': case 'c': idx += pow(4, (len -i -1)) * 1; break;
case 'G': case 'g': idx += pow(4, (len -i -1)) * 2; break;
case 'T': case 't': idx += pow(4, (len -i -1)) * 3; break;
default: return -1;
}
}
return idx;
}
int gkn_str2idx(const char *str) {
return gkn_mem2idx(str, 0, strlen(str));
}
char * gkn_idx2str(int val, int len) {
char dna[4] = "ACGT";
char *str = malloc(len + 1);
str[len] = '\0';
for (int i = 0; i < len; i++) {
int max = pow(4, (len-i-1));
int r = 0;
if (val > max -1) {
r = val / max;
val -= r * max;
}
str[i] = dna[r];
}
return str;
}
char * gkn_revcomp (const char *seq) {
int length = strlen(seq);
char *str = gkn_malloc(length +1);
str[strlen(seq)] = '\0';
for (int i = 1; i <= length; i++) {
switch (seq[i-1]) {
case 'A': str[length -i] = 'T'; break;
case 'a': str[length -i] = 't'; break;
case 'C': str[length -i] = 'G'; break;
case 'c': str[length -i] = 'g'; break;
case 'G': str[length -i] = 'C'; break;
case 'g': str[length -i] = 'c'; break;
case 'T': str[length -i] = 'A'; break;
case 't': str[length -i] = 'a'; break;
case 'N': str[length -i] = 'N'; break;
case 'n': str[length -i] = 'n'; break;
case 'R': str[length -i] = 'Y'; break;
case 'r': str[length -i] = 'y'; break;
case 'Y': str[length -i] = 'R'; break;
case 'y': str[length -i] = 'r'; break;
case 'W': str[length -i] = 'S'; break;
case 'w': str[length -i] = 's'; break;
case 'S': str[length -i] = 'W'; break;
case 's': str[length -i] = 'w'; break;
case 'K': str[length -i] = 'M'; break;
case 'k': str[length -i] = 'm'; break;
case 'M': str[length -i] = 'K'; break;
case 'm': str[length -i] = 'k'; break;
case 'B': str[length -i] = 'V'; break;
case 'b': str[length -i] = 'v'; break;
case 'D': str[length -i] = 'H'; break;
case 'd': str[length -i] = 'h'; break;
case 'H': str[length -i] = 'D'; break;
case 'h': str[length -i] = 'd'; break;
case 'V': str[length -i] = 'B'; break;
case 'v': str[length -i] = 'b'; break;
default: gkn_exit("alphabet error %c", seq[i-1]);
}
}
return str;
}
// FASTA file
void gkn_fasta_free(gkn_fasta ff) {
free(ff->def);
free(ff->seq);
free(ff);
}
gkn_fasta gkn_fasta_new (const char *def, const char *seq) {
gkn_fasta ff = gkn_malloc(sizeof(struct gkn_FASTA));
ff->def = gkn_malloc(strlen(def) +1);
ff->seq = gkn_malloc(strlen(seq) +1);
ff->length = strlen(seq);
strcpy(ff->def, def);
strcpy(ff->seq, seq);
return ff;
}
gkn_fasta gkn_fasta_read(gkn_pipe io) {
// check for fasta header
char c = fgetc(io->stream);
ungetc(c, io->stream);
if (c == EOF || (unsigned char)c == 255) return NULL;
if (c != '>') gkn_exit("fasta? %c %d", c, (int)c);
// def
char *def = gkn_readline(io);
// seq
gkn_vec lines = gkn_vec_new();
while (1) {
char c = fgetc(io->stream);
ungetc(c, io->stream);
if (c == EOF || (unsigned char)c == 255 || c == '>' ) break;
char *line = gkn_readline(io);
if (line == NULL) break;
gkn_vec_push(lines, line);
}
int letters = 0;
for (int i = 0; i < lines->size; i++) {
char *line = lines->elem[i];
letters += strlen(line);
}
char *seq = malloc(letters + 1);
int off = 0;
for (int i = 0; i < lines->size; i++) {
char *line = lines->elem[i];
strcpy(seq + off, line);
off += strlen(line);
}
// clean up
for (int i = 0; i < lines->size; i++) {
free(lines->elem[i]);
}
gkn_vec_free(lines);
// return object
gkn_fasta ff = malloc(sizeof(struct gkn_FASTA));
ff->def = def;
ff->seq = seq;
ff->length = strlen(seq);
return ff;
}
static int FASTA_LINE_LENGTH = 80;
void gkn_fasta_write(FILE *stream, const gkn_fasta ff) {
if (ff->def[0] != '>') fprintf(stream, ">");
fprintf(stream, "%s", ff->def);
if (ff->def[strlen(ff->def) -1] != '\n') fprintf(stream, "\n");
for (int i = 0; i < ff->length; i++) {
fputc(ff->seq[i], stream);
if ((i+1) % FASTA_LINE_LENGTH == 0) fprintf(stream, "\n");
}
fprintf(stream, "\n");
}
void gkn_fasta_set_line_length (int length) {
FASTA_LINE_LENGTH = length;
}
#endif