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#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include "seq.h"
static int SEQ_BLOCK_SIZE = 512;
void seq_set_block_size(int size)
{
SEQ_BLOCK_SIZE = size;
}
/* Read sequences from file "fp" in FASTA format. Sequence will be saved
* in "seq", sequence ID in "locus", and comment saved in "comment",
* provided "comment != 0". Sequence length will be returned. If -1 is
* returned, no sequence is left in the file. */
int seq_read_fasta(FILE *fp, seq_t *seq, char *locus, char *comment)
{
int c, l, max;
char *p;
c = 0;
while (!feof(fp) && fgetc(fp) != '>');
if (feof(fp)) return -1;
p = locus;
while (!feof(fp) && (c = fgetc(fp)) != ' ' && c != '\t' && c != '\n')
if (c != '\r') *p++ = c;
*p = '\0';
if (comment) {
p = comment;
if (c != '\n') {
while (!feof(fp) && ((c = fgetc(fp)) == ' ' || c == '\t'));
if (c != '\n') {
*p++ = c;
while (!feof(fp) && (c = fgetc(fp)) != '\n')
if (c != '\r') *p++ = c;
}
}
*p = '\0';
} else if (c != '\n') while (!feof(fp) && fgetc(fp) != '\n');
l = 0; max = seq->m;
while (!feof(fp) && (c = fgetc(fp)) != '>') {
if (isalpha(c) || c == '-' || c == '.') {
if (l + 1 >= max) {
max += SEQ_BLOCK_SIZE;
seq->s = (unsigned char*)realloc(seq->s, sizeof(char) * max);
}
seq->s[l++] = (unsigned char)c;
}
}
if (c == '>') ungetc(c,fp);
seq->s[l] = 0;
seq->m = max; seq->l = l;
return l;
}
int seq_read_fastq(FILE *fp, seq_t *seq, seq_t *qual, char *name)
{
int c, l, max;
char *p;
c = 0;
/* first read the sequence */
while (!feof(fp) && fgetc(fp) != '@');
if (feof(fp)) return -1;
p = name;
while (!feof(fp) && (c = fgetc(fp)) != ' ' && c != '\t' && c != '\n')
if (c != '\r') *p++ = c;
*p = '\0';
if (c != '\n') while (!feof(fp) && fgetc(fp) != '\n');
l = 0; max = seq->m;
while (!feof(fp) && (c = fgetc(fp)) != '+') {
if (isalpha(c) || c == '-' || c == '.') {
if (l + 1 >= max) {
max += SEQ_BLOCK_SIZE;
seq->s = (unsigned char*)realloc(seq->s, sizeof(char) * max);
}
seq->s[l++] = (unsigned char)c;
}
}
if (c == '+') ungetc(c, fp);
seq->s[l] = 0;
seq->m = max; seq->l = l;
/* now come to the qualities */
while (!feof(fp) && fgetc(fp) != '+');
p = name;
while (!feof(fp) && (c = fgetc(fp)) != ' ' && c != '\t' && c != '\n')
if (c != '\r' && *p++ != c) {
fprintf(stderr, "[seq_read_fastq] Inconsistent sequence name: %s. Continue anyway.\n", name);
return seq->l;
}
l = 0; max = qual->m;
while (!feof(fp) && l < seq->l) {
c = fgetc(fp);
if (c >= 33 && c < 127) {
if (l + 1 >= max) {
max += SEQ_BLOCK_SIZE;
qual->s = (unsigned char*)realloc(qual->s, sizeof(char) * max);
}
qual->s[l++] = (unsigned char)(c - 33);
}
}
c = fgetc(fp);
if (c == '@') ungetc(c, fp);
qual->s[l] = 0;
qual->m = max; qual->l = l;
if (seq->l != qual->l)
fprintf(stderr, "[seq_read_fastq] Inconsistent length: %d!=%d. Continue anyway.", seq->l, qual->l);
return seq->l;
}
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