int seq_read_fasta(SEQ *seq)
{
int b, c;
charvec_t shdr = charvec_INIT(ckrealloc,ckfree);
charvec_t sseq = charvec_INIT(ckrealloc,ckfree);
if (feof(seq->fp) || ferror(seq->fp))
return 0;
if (seq->count > 0) {
if (seq->flags & SEQ_IS_SUBRANGE) {
return 0;
} else {
seq->from = 1;
seq->slen = -1; /* will be computed below */
}
}
if (seq->header) ZFREE(seq->header);
if (seq->seq) ZFREE(seq->seq);
seq->offset = ftell(seq->fp);
/* --- header --- */
c = getnwc(seq->fp);
if (c == '>') {
while (c != '\n' && c != EOF) {
char_append(&shdr, c);
c = getc(seq->fp);
}
} else {
un_getc(c, seq->fp);
}
if (ferror(seq->fp))
Fatalfr("seq_read(%s)", seq->fname);
char_append(&shdr, 0);
seq->header = shdr.a;
seq->hlen = shdr.len;
/* --- seq --- */
b = '\n';
c = getnwc(seq->fp);
while ((c != EOF) && !(b == '\n' && c == '>')) {
switch (nfasta_ctype[c]) {
case Nfasta_nt:
char_append(&sseq, c);
break;
case Nfasta_ws:
/* skip space */
break;
case Nfasta_amb:
if (seq->flags & SEQ_ALLOW_AMB) {
char_append(&sseq, c);
break;
}
/* FALLTHRU */
default:
fatalf("non-DNA character '%c' in sequence '%s'",
c, seq->fname);
break;
}
b = c;
c = getc(seq->fp);
}
un_getc(c, seq->fp);
if (ferror(seq->fp))
Fatalfr("seq_read(%s)", seq->fname);
/* check conformance */
if (SEQ_LEN(seq) == -1) {
char_append(&sseq, 0);
charvec_fit(&sseq);
seq->seq = (uchar*)sseq.a;
seq->slen = sseq.len;
if (seq->slen > 0) --seq->slen; /* don't include '\0' */
} else {
charvec_t ssub = charvec_INIT(ckrealloc,ckfree);
int i;
if (SEQ_FROM(seq) < 1 ||
(int)sseq.len < SEQ_FROM(seq) ||
SEQ_TO(seq) < 1 ||
(int)sseq.len < SEQ_TO(seq) ||
SEQ_TO(seq) < SEQ_FROM(seq))
fatalf("range [%d,%d] incommensurate with sequence [%d,%d]",
SEQ_FROM(seq), SEQ_TO(seq), 1, sseq.len);
for (i = SEQ_FROM(seq); i <= SEQ_TO(seq); ++i)
char_append(&ssub, sseq.a[i-1]);
char_append(&ssub, 0);
charvec_fini(&sseq);
seq->seq = (uchar*)ssub.a;
}
seq->flags = seq->flags &~ SEQ_IS_REVCOMP;
if (seq->flags & SEQ_DO_REVCOMP) {
(void)seq_revcomp_inplace(seq);
}
if (seq->flags & SEQ_HAS_MASK) {
(void)seq_mask_inplace(seq);
}
seq->count++;
return 1;
}
int
main(int argc, char *argv[])
{
int count;
seq_t seq1, seq2;
hash_env_t he;
collec_t res, rev_res;
#if defined(DEBUG) && (DEBUG > 1)
mcheck(NULL);
mtrace();
#endif
argv0 = argv[0];
if (setlocale(LC_ALL, "POSIX") == NULL)
fprintf(stderr, "%s: Warning: could not set locale to POSIX\n", argv[0]);
signal(SIGSEGV, bug_handler);
#ifndef __MINGW32__
signal(SIGBUS, bug_handler);
#endif
/* Default options. */
options.C = DEFAULT_C;
options.cutoff = DIST_CUTOFF;
options.gapPct = DEFAULT_GAPPCT;
options.intron_window = 6;
options.K = DEFAULT_K;
options.splice_type_list = "GTAG,GCAG,GTAC,ATAC";
options.nbSplice = 4;
options.scoreSplice_window = 10;
options.mismatchScore = MISMATCH;
options.reverse = 2;
options.matchScore = MATCH;
options.W = DEFAULT_W;
options.X = DEFAULT_X;
options.filterPct = DEFAULT_FILTER;
options.minScore_cutoff = MATCH_CUTOFF;
while (1) {
int c = getopt(argc, argv, "A:C:c:E:f:g:I:K:L:M:o:q:R:r:W:X:");
if (c == -1)
break;
switch (c) {
case 'A':
options.ali_flag = atoi(optarg);
if (options.ali_flag < 0 || options.ali_flag > 4)
fatal("A must be one of 0, 1, 2, 3, or 4.\n");
break;
case 'C': {
int val = atoi(optarg);
if (val < 0)
fatal("Value for option C must be non-negative.\n");
options.C = val;
break;
}
case 'c': {
int val = atoi(optarg);
if (val < 0)
fatal("Value for option c must be non-negative.\n");
options.minScore_cutoff = val;
break;
}
case 'E':
options.cutoff = atoi(optarg);
if (options.cutoff < 3 || options.cutoff > 10)
fatal("Cutoff (E) must be within [3,10].\n");
break;
case 'f':
options.filterPct = atoi(optarg);
if (options.filterPct > 100)
fatal("Filter in percent (f) must be within [0,100].\n");
break;
case 'g':
options.gapPct = atoi(optarg);
break;
case 'I':
options.intron_window = atoi(optarg);
break;
case 'K': {
int val = atoi(optarg);
if (val < 0)
fatal("Value for option K must be non-negative.\n");
options.K = val;
break;
}
case 'L': {
size_t i;
size_t len = strlen(optarg);
options.splice_type_list = optarg;
options.nbSplice = 1;
if (len % 5 != 4)
fatal("Splice types list has illegal length (%zu)\n", len);
for (i = 0; i < len; i++)
if (i % 5 == 4) {
if (options.splice_type_list[i] != ',')
fatal("Comma expected instead of %c at position %zu"
"in splice types list.\n",
options.splice_type_list[i], i);
options.nbSplice += 1;
} else {
if (options.splice_type_list[i] != 'A'
&& options.splice_type_list[i] != 'C'
&& options.splice_type_list[i] != 'G'
&& options.splice_type_list[i] != 'T')
fatal("Expected 'A', 'C', 'G' or 'T' instead of '%c' at"
"position %zu in splice types list.\n",
options.splice_type_list[i], i);
}
break;
}
case 'M': {
int val = atoi(optarg);
if (val < 0)
fatal("Value for option M must be non-negative.\n");
options.scoreSplice_window = val;
break;
}
case 'o':
options.dnaOffset = atoi(optarg);
break;
case 'q':
options.mismatchScore = atoi(optarg);
break;
case 'R':
options.reverse = atoi(optarg);
if (options.reverse < 0 || options.reverse > 2)
fatal("R must be one of 0, 1, or 2.\n");
break;
case 'r':
options.matchScore = atoi(optarg);
break;
case 'W':
options.W = atoi(optarg);
if (options.W < 1 || options.W > 15)
fatal("W must be within [1,15].\n");
break;
case 'X':
options.X = atoi(optarg);
if (options.X < 1)
fatal("X must be positive.\n");
break;
case '?':
break;
default:
fprintf(stderr, "?? getopt returned character code 0%o ??\n", c);
}
}
if (optind + 2 != argc) {
fprintf(stderr, Usage, argv[0], options.ali_flag, options.C,
options.minScore_cutoff, options.cutoff,
options.filterPct, options.gapPct, options.intron_window,
options.K, options.splice_type_list, options.scoreSplice_window,
options.dnaOffset, options.mismatchScore, options.reverse,
options.matchScore, options.W, options.X);
return 1;
}
/* read seq1 */
init_seq(argv[optind], &seq1);
if (get_next_seq(&seq1, options.dnaOffset, 1) != 0)
fatal("Cannot read sequence from %s.\n", argv[optind]);
strncpy(dna_seq_head, seq1.header, 256);
/* read seq2 */
init_seq(argv[optind + 1], &seq2);
if (get_next_seq(&seq2, 0, 0) != 0)
fatal("Cannot read sequence from %s.\n", argv[optind + 1]);
init_encoding();
init_hash_env(&he, options.W, seq1.seq, seq1.len);
init_col(&res, 1);
init_col(&rev_res, 1);
bld_table(&he);
init_splice_junctions();
count = 0;
while (!count || get_next_seq(&seq2, 0, 0) == 0) {
unsigned int curRes;
strncpy(rna_seq_head, seq2.header, 256);
++count;
switch (options.reverse) {
case 0:
SIM4(&he, &seq2, &res);
break;
case 2:
SIM4(&he, &seq2, &res);
case 1:
seq_revcomp_inplace(&seq2);
SIM4(&he, &seq2, &rev_res);
break;
default:
fatal ("Unrecognized request for EST orientation.\n");
}
/* Keep only the best matches, according to filterPct. */
if (options.filterPct > 0) {
unsigned int max_nmatches = 0;
for (curRes = 0; curRes < rev_res.nb; curRes++) {
result_p_t r = rev_res.e.result[curRes];
if (r->st.nmatches > max_nmatches)
max_nmatches = r->st.nmatches;
}
for (curRes = 0; curRes < res.nb; curRes++) {
result_p_t r = res.e.result[curRes];
if (r->st.nmatches > max_nmatches)
max_nmatches = r->st.nmatches;
}
max_nmatches = (max_nmatches * options.filterPct) / 100;
for (curRes = 0; curRes < rev_res.nb; curRes++) {
result_p_t r = rev_res.e.result[curRes];
if (r->st.nmatches < max_nmatches)
r->st.nmatches = 0;
}
for (curRes = 0; curRes < res.nb; curRes++) {
result_p_t r = res.e.result[curRes];
if (r->st.nmatches < max_nmatches)
r->st.nmatches = 0;
}
}
/* Now, print results. */
for (curRes = 0; curRes < rev_res.nb; curRes++)
print_res(rev_res.e.result[curRes], 1, &seq1, &seq2);
rev_res.nb = 0;
if (options.reverse && options.ali_flag)
/* reverse-complement back seq2 for alignment */
seq_revcomp_inplace(&seq2);
for (curRes = 0; curRes < res.nb; curRes++)
print_res(res.e.result[curRes], 0, &seq1, &seq2);
res.nb = 0;
}
#ifdef DEBUG
fprintf(stderr, "DEBUG mode: freeing all memory...\n");
fflush(stdout);
fflush(stderr);
free_hash_env(&he);
free_seq(&seq1);
free_seq(&seq2);
free(options.splice);
free(res.e.elt);
free(rev_res.e.elt);
#endif
return 0;
}