static int show_entry(GtStr *description, GtStr *sequence, bool translate,
GtUword width, GtFile *outfp)
{
int had_err = 0;
if (translate) {
GtTranslatorStatus status;
unsigned int frame;
char translated;
GtStr *protein = gt_str_new();
GtCodonIterator *ci = gt_codon_iterator_simple_new(gt_str_get(sequence),
gt_str_length(sequence),
NULL);
GtTranslator* tr = gt_translator_new(ci);
status = gt_translator_next(tr, &translated, &frame, NULL);
while (status == GT_TRANSLATOR_OK) {
if (frame == 0)
gt_str_append_char(protein, translated);
status = gt_translator_next(tr, &translated, &frame, NULL);
}
if (status == GT_TRANSLATOR_ERROR)
had_err = -1;
gt_fasta_show_entry(gt_str_get(description), gt_str_get(protein),
gt_str_length(protein), width, outfp);
gt_str_delete(protein);
gt_translator_delete(tr);
gt_codon_iterator_delete(ci);
}
else {
gt_fasta_show_entry(gt_str_get(description), gt_str_get(sequence),
gt_str_length(sequence), width, outfp);
}
return had_err;
}
static int translate_dna_lua(lua_State *L)
{
GtStr *protein;
GtTranslator *tr;
int rval;
char translated;
unsigned int frame;
const char *dna = luaL_checkstring(L, 1);
protein = gt_str_new();
GtCodonIterator *ci = gt_codon_iterator_simple_new(dna,
strlen(dna),
NULL);
tr = gt_translator_new(ci);
rval = gt_translator_next(tr, &translated, &frame, NULL);
while (!rval && translated) {
gt_str_append_char(protein, translated);
rval = gt_translator_next(tr, &translated, &frame, NULL);
}
lua_pushstring(L, gt_str_get(protein));
gt_str_delete(protein);
gt_translator_delete(tr);
gt_codon_iterator_delete(ci);
return 1;
}
int gt_extract_and_translate_feature_sequence(GtFeatureNode *feature_node,
const char *type,
bool join,
GtRegionMapping *rm,
GtTransTable *ttable,
GtStr *translation_fr1,
GtStr *translation_fr2,
GtStr *translation_fr3,
GtError *err)
{
GtTranslator *tr = NULL;
GtTranslatorStatus status;
GtCodonIterator *ci = NULL;
unsigned int frame, phase_offset = 0;
char translated;
int had_err = 0;
GtStr *sequence = gt_str_new();
gt_assert(feature_node && type);
had_err = gt_extract_feature_sequence_generic(sequence,
(GtGenomeNode*) feature_node,
type, join, NULL, NULL,
&phase_offset, rm, err);
/* do translation if we have at least one codon */
if (!had_err && gt_str_length(sequence) > phase_offset + 2) {
ci = gt_codon_iterator_simple_new(gt_str_get(sequence) + phase_offset,
gt_str_length(sequence) - phase_offset,
NULL);
tr = gt_translator_new(ci);
if (ttable)
gt_translator_set_translation_table(tr, ttable);
status = gt_translator_next(tr, &translated, &frame, NULL);
while (status == GT_TRANSLATOR_OK) {
if (frame == 0 && translation_fr1)
gt_str_append_char(translation_fr1, translated);
else if (frame == 1 && translation_fr2)
gt_str_append_char(translation_fr2, translated);
else if (frame == 2 && translation_fr3)
gt_str_append_char(translation_fr3, translated);
status = gt_translator_next(tr, &translated, &frame, NULL);
}
if (status == GT_TRANSLATOR_ERROR)
had_err = -1;
}
gt_translator_delete(tr);
gt_codon_iterator_delete(ci);
gt_str_delete(sequence);
return had_err;
}
static int gt_seqtranslate_do_translation(GtTranslateArguments *arguments,
const char *sequence,
GtUword length,
const char *desc,
GtStr **translations,
bool rev,
GtError *err)
{
GtTranslator *tr;
GT_UNUSED GtTranslatorStatus trst;
GtCodonIterator *ci;
char translated;
int had_err = 0;
GtStr *str;
unsigned int frame,
i;
ci = gt_codon_iterator_simple_new(sequence, length, err);
tr = gt_translator_new(ci);
trst = gt_translator_next(tr, &translated, &frame, err);
while (trst == GT_TRANSLATOR_OK) {
gt_str_append_char(translations[frame], translated);
trst = gt_translator_next(tr, &translated, &frame, err);
}
gt_codon_iterator_delete(ci);
gt_translator_delete(tr);
if (trst == GT_TRANSLATOR_ERROR)
return -1;
str = gt_str_new();
for (i = 0; i < 3; i++) {
if (gt_str_length(translations[i]) > 0) {
gt_str_append_cstr(str, desc);
gt_str_append_cstr(str, " (");
gt_str_append_ulong(str, i+1);
gt_str_append_cstr(str, rev ? "-" : "+");
gt_str_append_cstr(str, ")");
gt_fasta_show_entry(gt_str_get(str), gt_str_get(translations[i]),
gt_str_length(translations[i]),
arguments->fasta_width, arguments->outfp);
gt_str_reset(translations[i]);
gt_str_reset(str);
}
}
gt_str_delete(str);
return had_err;
}
int gt_translator_unit_test(GtError *err)
{
int had_err = 0;
GtTranslatorStatus test_errnum;
GtTranslator *tr;
GtCodonIterator *ci;
GtError *test_err;
GtStrArray *codons, *invalidcodons;
const char *seq = "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGT"
"GGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGT"
"TACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG";
const char *no_startcodon = "AAAAAAAAAATCATCTCCCCATTTTTTT";
const char *invalidseq = "ZAGCTTTTCATTCTGACTGCAAATATGTCTCTGTGT";
const char *invalidseq2 = "AGCTTTTCATTCTGACZTGCAAATATGTCTCTGTGT";
char translated;
unsigned int frame;
GtUword pos = 0;
GtStr *protein[3];
gt_error_check(err);
test_err = gt_error_new();
ci = gt_codon_iterator_simple_new(seq, (GtUword) strlen(seq), test_err);
tr = gt_translator_new(ci);
protein[0] = gt_str_new();
protein[1] = gt_str_new();
protein[2] = gt_str_new();
codons = gt_str_array_new();
gt_str_array_add_cstr(codons, "ACG");
gt_str_array_add_cstr(codons, "ACT");
invalidcodons = gt_str_array_new();
gt_str_array_add_cstr(invalidcodons, "ACG");
gt_str_array_add_cstr(invalidcodons, "AC");
/* do 3-frame translation */
gt_error_unset(test_err);
test_errnum = gt_translator_next(tr, &translated, &frame, test_err);
while (!test_errnum && translated) {
gt_str_append_char(protein[frame], translated);
test_errnum = gt_translator_next(tr, &translated, &frame, test_err);
gt_ensure(
test_errnum != GT_TRANSLATOR_ERROR && !gt_error_is_set(test_err));
}
gt_ensure(
test_errnum == GT_TRANSLATOR_END && !gt_error_is_set(test_err));
/* check 3-frame translation */
gt_ensure(strcmp(gt_str_get(protein[0]),
"SFSF*LQRAICLCVD*KKSV**QLLNWLPAVSKLKFY*LR") == 0);
gt_ensure(strcmp(gt_str_get(protein[1]),
"AFHSDCNGQYVSVWIKKRVSDSSF*TGYLP*VN*NFIDL") == 0);
gt_ensure(strcmp(gt_str_get(protein[2]),
"LFILTATGNMSLCGLKKECLIAASELVTCRE*IKILLT*") == 0);
/* find start codon -- positive */
gt_error_unset(test_err);
gt_codon_iterator_rewind(ci);
test_errnum = gt_translator_find_startcodon(tr, &pos, test_err);
gt_ensure(!test_errnum && !gt_error_is_set(test_err));
gt_ensure(pos == 11UL);
/* find stop codon -- positive */
gt_error_unset(test_err);
gt_codon_iterator_rewind(ci);
test_errnum = gt_translator_find_stopcodon(tr, &pos, test_err);
gt_ensure(!test_errnum && !gt_error_is_set(test_err));
gt_ensure(pos == 12UL);
/* find arbitrary codons -- positive */
gt_error_unset(test_err);
gt_codon_iterator_rewind(ci);
test_errnum = gt_translator_find_codon(tr, codons, &pos, test_err);
gt_ensure(!test_errnum && !gt_error_is_set(test_err));
gt_ensure(pos == 14UL);
/* find arbitrary codons -- negative (invalid codons) */
gt_error_unset(test_err);
gt_codon_iterator_rewind(ci);
test_errnum = gt_translator_find_codon(tr, invalidcodons, &pos, test_err);
gt_ensure(
test_errnum == GT_TRANSLATOR_ERROR && gt_error_is_set(test_err));
gt_error_unset(test_err);
gt_codon_iterator_delete(ci);
ci = gt_codon_iterator_simple_new(invalidseq,
(GtUword) strlen(invalidseq),
test_err);
gt_ensure(ci && !gt_error_is_set(test_err));
gt_translator_reset(tr, ci);
/* check translation of sequence with invalid beginning */
test_errnum = gt_translator_next(tr, &translated, &frame, test_err);
gt_ensure(test_errnum && gt_error_is_set(test_err));
/* check translation of sequence with invalid character within */
gt_error_unset(test_err);
gt_codon_iterator_delete(ci);
ci = gt_codon_iterator_simple_new(invalidseq2,
(GtUword) strlen(invalidseq2),
test_err);
gt_ensure(ci && !gt_error_is_set(test_err));
gt_translator_reset(tr, ci);
test_errnum = gt_translator_next(tr, &translated, &frame, test_err);
while (!test_errnum && translated) {
gt_str_append_char(protein[frame], translated);
test_errnum = gt_translator_next(tr, &translated, &frame, test_err);
}
gt_ensure(
test_errnum == GT_TRANSLATOR_ERROR && gt_error_is_set(test_err));
/* find start codon -- fail */
gt_error_unset(test_err);
gt_codon_iterator_delete(ci);
ci = gt_codon_iterator_simple_new(no_startcodon,
(GtUword) strlen(no_startcodon),
test_err);
gt_ensure(ci && !gt_error_is_set(test_err));
gt_translator_reset(tr, ci);
test_errnum = gt_translator_find_startcodon(tr, &pos, test_err);
gt_ensure(
test_errnum == GT_TRANSLATOR_END && !gt_error_is_set(test_err));
/* find stop codon -- fail */
gt_error_unset(test_err);
gt_codon_iterator_rewind(ci);
test_errnum = gt_translator_find_stopcodon(tr, &pos, test_err);
gt_ensure(
test_errnum == GT_TRANSLATOR_END && !gt_error_is_set(test_err));
/* find arbitrary codons -- negative (none there) */
gt_error_unset(test_err);
gt_codon_iterator_rewind(ci);
test_errnum = gt_translator_find_codon(tr, codons, &pos, test_err);
gt_ensure(
test_errnum == GT_TRANSLATOR_END && !gt_error_is_set(test_err));
gt_codon_iterator_delete(ci);
gt_translator_delete(tr);
gt_str_delete(protein[0]);
gt_str_delete(protein[1]);
gt_str_delete(protein[2]);
gt_str_array_delete(codons);
gt_str_array_delete(invalidcodons);
gt_error_delete(test_err);
return had_err;
}
static int gt_ltrdigest_pdom_visitor_feature_node(GtNodeVisitor *nv,
GtFeatureNode *fn,
GtError *err)
{
GtLTRdigestPdomVisitor *lv;
GtFeatureNodeIterator *fni;
GtFeatureNode *curnode = NULL;
int had_err = 0;
GtRange rng;
GtUword i;
lv = gt_ltrdigest_pdom_visitor_cast(nv);
gt_assert(lv);
gt_error_check(err);
/* traverse annotation subgraph and find LTR element */
fni = gt_feature_node_iterator_new(fn);
while (!had_err && (curnode = gt_feature_node_iterator_next(fni))) {
if (strcmp(gt_feature_node_get_type(curnode), lv->root_type) == 0) {
lv->ltr_retrotrans = curnode;
}
}
gt_feature_node_iterator_delete(fni);
if (!had_err && lv->ltr_retrotrans != NULL) {
GtCodonIterator *ci;
GtTranslator *tr;
GtTranslatorStatus status;
GtUword seqlen;
char translated, *rev_seq;
#ifndef _WIN32
FILE *instream;
GtHMMERParseStatus *pstatus;
#endif
unsigned int frame;
GtStr *seq;
seq = gt_str_new();
rng = gt_genome_node_get_range((GtGenomeNode*) lv->ltr_retrotrans);
lv->leftLTR_5 = rng.start - 1;
lv->rightLTR_3 = rng.end - 1;
seqlen = gt_range_length(&rng);
had_err = gt_extract_feature_sequence(seq,
(GtGenomeNode*) lv->ltr_retrotrans,
lv->root_type,
false, NULL, NULL, lv->rmap, err);
if (!had_err) {
for (i = 0UL; i < 3UL; i++) {
gt_str_reset(lv->fwd[i]);
gt_str_reset(lv->rev[i]);
}
/* create translations */
ci = gt_codon_iterator_simple_new(gt_str_get(seq), seqlen, NULL);
gt_assert(ci);
tr = gt_translator_new(ci);
status = gt_translator_next(tr, &translated, &frame, err);
while (status == GT_TRANSLATOR_OK && translated) {
gt_str_append_char(lv->fwd[frame], translated);
status = gt_translator_next(tr, &translated, &frame, NULL);
}
if (status == GT_TRANSLATOR_ERROR) had_err = -1;
if (!had_err) {
rev_seq = gt_malloc((size_t) seqlen * sizeof (char));
strncpy(rev_seq, gt_str_get(seq), (size_t) seqlen * sizeof (char));
(void) gt_reverse_complement(rev_seq, seqlen, NULL);
gt_codon_iterator_delete(ci);
ci = gt_codon_iterator_simple_new(rev_seq, seqlen, NULL);
gt_translator_set_codon_iterator(tr, ci);
status = gt_translator_next(tr, &translated, &frame, err);
while (status == GT_TRANSLATOR_OK && translated) {
gt_str_append_char(lv->rev[frame], translated);
status = gt_translator_next(tr, &translated, &frame, NULL);
}
if (status == GT_TRANSLATOR_ERROR) had_err = -1;
gt_free(rev_seq);
}
gt_codon_iterator_delete(ci);
gt_translator_delete(tr);
}
/* run HMMER and handle results */
if (!had_err) {
#ifndef _WIN32
int pid, pc[2], cp[2];
GT_UNUSED int rval;
(void) signal(SIGCHLD, SIG_IGN); /* XXX: for now, ignore child's
exit status */
rval = pipe(pc);
gt_assert(rval == 0);
rval = pipe(cp);
gt_assert(rval == 0);
switch ((pid = (int) fork())) {
case -1:
perror("Can't fork");
exit(1); /* XXX: error handling */
case 0: /* child */
(void) close(1); /* close current stdout. */
rval = dup(cp[1]); /* make stdout go to write end of pipe. */
(void) close(0); /* close current stdin. */
rval = dup(pc[0]); /* make stdin come from read end of pipe. */
(void) close(pc[0]);
(void) close(pc[1]);
(void) close(cp[0]);
(void) close(cp[1]);
(void) execvp("hmmscan", lv->args); /* XXX: read path from env */
perror("couldn't execute hmmscan!");
exit(1);
default: /* parent */
for (i = 0UL; i < 3UL; i++) {
char buf[5];
GT_UNUSED ssize_t written;
(void) sprintf(buf, ">"GT_WU"%c\n", i, '+');
written = write(pc[1], buf, 4 * sizeof (char));
written = write(pc[1], gt_str_get(lv->fwd[i]),
(size_t) gt_str_length(lv->fwd[i]) * sizeof (char));
written = write(pc[1], "\n", 1 * sizeof (char));
(void) sprintf(buf, ">"GT_WU"%c\n", i, '-');
written = write(pc[1], buf, 4 * sizeof (char));
written = write(pc[1], gt_str_get(lv->rev[i]),
(size_t) gt_str_length(lv->rev[i]) * sizeof (char));
written = write(pc[1], "\n", 1 * sizeof (char));
}
(void) close(pc[0]);
(void) close(pc[1]);
(void) close(cp[1]);
instream = fdopen(cp[0], "r");
pstatus = gt_hmmer_parse_status_new();
had_err = gt_ltrdigest_pdom_visitor_parse_output(lv, pstatus,
instream, err);
(void) fclose(instream);
if (!had_err)
had_err = gt_ltrdigest_pdom_visitor_process_hits(lv, pstatus, err);
gt_hmmer_parse_status_delete(pstatus);
}
#else
/* XXX */
gt_error_set(err, "HMMER call not implemented on Windows\n");
had_err = -1;
#endif
}
gt_str_delete(seq);
}
if (!had_err)
had_err = gt_ltrdigest_pdom_visitor_choose_strand(lv);
return had_err;
}
void gt_outputtranslationandorf(unsigned long pglnum, const GthAGS *ags,
unsigned long agsnum,
unsigned long translationtable,
GthInput *input,
unsigned int indentlevel,
GthOutput *out)
{
unsigned long i;
unsigned int nframe;
const unsigned char *gen_seq_orig;
GtStr *frame[3];
char translated;
GtTranslatorStatus status;
GtTranslator *translator;
GtTransTable *transtable;
GtCodonIterator *ci;
GthSplicedSeq *spliced_seq;
GtArray *ranges;
GtFile *outfp = out->outfp;
/* output header */
if (out->xmlout) {
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<three_phase_translation "
"xmlns=\"http://www.genomethreader.org/GTH_output/"
"PGL_module/predicted_gene_location/AGS_information/"
"three_phase_translation/\">\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<description PGL_serial=\"%lu\" "
"AGS_serial=\"%lu\" gDNA_strand=\"%c\"/>\n",
pglnum + OUTPUTOFFSET, agsnum + OUTPUTOFFSET,
SHOWSTRAND(gth_ags_is_forward(ags)));
}
else {
gt_file_xprintf(outfp, "3-phase translation of AGS-%lu (%cstrand):\n\n",
agsnum + OUTPUTOFFSET,
SHOWSTRAND(gth_ags_is_forward(ags)));
}
ranges = gt_array_new(sizeof (GtRange));
for (i = 0; i < gt_array_size(ags->exons); i++)
gt_array_add(ranges, ((GthExonAGS*) gt_array_get(ags->exons, i))->range);
/* get genomic sequence */
gen_seq_orig = gth_input_original_genomic_sequence(input,
gth_ags_filenum(ags),
gth_ags_is_forward(ags));
spliced_seq = gth_spliced_seq_new(gen_seq_orig, ranges);
frame[0] = gt_str_new();
frame[1] = gt_str_new();
frame[2] = gt_str_new();
/* prepare for translation */
ci = gt_codon_iterator_simple_new((const char*) spliced_seq->splicedseq,
spliced_seq->splicedseqlen, NULL);
gt_assert(ci);
transtable = gt_trans_table_new(translationtable, NULL);
gt_assert(transtable);
/* translate the template in all three frames */
translator = gt_translator_new_with_table(transtable, ci);
status = gt_translator_next(translator, &translated, &nframe, NULL);
while (status == GT_TRANSLATOR_OK) {
gt_str_append_char(frame[nframe], translated);
status = gt_translator_next(translator, &translated, &nframe, NULL);
}
gt_assert(status != GT_TRANSLATOR_ERROR);
gt_translator_delete(translator);
gt_trans_table_delete(transtable);
gt_codon_iterator_delete(ci);
/* show the translation */
showtranslation(spliced_seq, gt_str_get(frame[0]), gt_str_get(frame[1]),
gt_str_get(frame[2]), ags->exons, gth_ags_is_forward(ags),
gth_ags_total_length(ags), gth_ags_genomic_offset(ags),
indentlevel, out);
/* show the (consolidated) ORFs */
gthshowORFs(gt_str_get(frame[0]), gt_str_get(frame[1]), gt_str_get(frame[2]),
gt_str_length(frame[0]), gt_str_length(frame[1]),
gt_str_length(frame[2]), gth_ags_is_forward(ags),
gth_ags_total_length(ags), gth_ags_genomic_offset(ags),
gt_str_get(ags->gen_id), pglnum, agsnum, spliced_seq,
indentlevel, out);
if (out->xmlout) {
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</three_phase_translation>\n");
}
gth_spliced_seq_delete(spliced_seq);
gt_array_delete(ranges);
gt_str_delete(frame[0]);
gt_str_delete(frame[1]);
gt_str_delete(frame[2]);
}
