static int gt_seqmutate_runner(int argc, const char **argv, int parsed_args,
void *tool_arguments, GtError *err)
{
MutateArguments *arguments = tool_arguments;
GtBioseqIterator *bsi;
unsigned long i;
GtBioseq *bioseq;
GtSeq *mutated_seq;
int had_err;
gt_error_check(err);
gt_assert(arguments);
bsi = gt_bioseq_iterator_new(argc - parsed_args, argv + parsed_args);
while (!(had_err = gt_bioseq_iterator_next(bsi, &bioseq, err)) && bioseq) {
for (i = 0; i < gt_bioseq_number_of_sequences(bioseq); i++) {
mutated_seq = gt_mutate_seq(gt_bioseq_get_description(bioseq, i),
gt_bioseq_get_sequence(bioseq, i),
gt_bioseq_get_sequence_length(bioseq, i),
gt_bioseq_get_alphabet(bioseq),
arguments->rate);
gt_fasta_show_entry(gt_seq_get_description(mutated_seq),
gt_seq_get_orig(mutated_seq),
gt_seq_length(mutated_seq),
arguments->width, arguments->outfp);
gt_seq_delete(mutated_seq);
}
gt_bioseq_delete(bioseq);
}
gt_bioseq_iterator_delete(bsi);
return had_err;
}
GtPBSResults* gt_pbs_find(const char *seq,
const char *rev_seq,
GtLTRElement *element,
GtPBSOptions *o,
GtError *err)
{
GtSeq *seq_forward, *seq_rev;
GtPBSResults *results;
unsigned long j;
GtAlignment *ali;
GtAlphabet *a = gt_alphabet_new_dna();
GtScoreFunction *sf = gt_dna_scorefunc_new(a,
o->ali_score_match,
o->ali_score_mismatch,
o->ali_score_insertion,
o->ali_score_deletion);
gt_assert(seq && rev_seq && sf && a && element);
results = gt_pbs_results_new(element, o);
seq_forward = gt_seq_new(seq + (gt_ltrelement_leftltrlen(element))
- (o->radius),
2*o->radius + 1,
a);
seq_rev = gt_seq_new(rev_seq + (gt_ltrelement_rightltrlen(element))
- (o->radius),
2*o->radius + 1,
a);
for (j=0;j<gt_bioseq_number_of_sequences(o->trna_lib);j++)
{
GtSeq *trna_seq, *trna_from3;
char *trna_from3_full;
unsigned long trna_seqlen;
trna_seq = gt_bioseq_get_seq(o->trna_lib, j);
trna_seqlen = gt_seq_length(trna_seq);
trna_from3_full = gt_calloc(trna_seqlen, sizeof (char));
memcpy(trna_from3_full, gt_seq_get_orig(trna_seq),
sizeof (char)*trna_seqlen);
(void) gt_reverse_complement(trna_from3_full, trna_seqlen, err);
trna_from3 = gt_seq_new_own(trna_from3_full, trna_seqlen, a);
ali = gt_swalign(seq_forward, trna_from3, sf);
gt_pbs_add_hit(results->hits, ali, o, trna_seqlen,
gt_seq_get_description(trna_seq), GT_STRAND_FORWARD,
results);
gt_alignment_delete(ali);
ali = gt_swalign(seq_rev, trna_from3, sf);
gt_pbs_add_hit(results->hits, ali, o, trna_seqlen,
gt_seq_get_description(trna_seq), GT_STRAND_REVERSE,
results);
gt_alignment_delete(ali);
gt_seq_delete(trna_from3);
}
gt_seq_delete(seq_forward);
gt_seq_delete(seq_rev);
gt_score_function_delete(sf);
gt_alphabet_delete(a);
gt_array_sort(results->hits, gt_pbs_hit_compare);
return results;
}
static GtMatchIteratorStatus gt_match_iterator_sw_next(GtMatchIterator *mi,
GT_UNUSED GtMatch **match,
GT_UNUSED GtError *err)
{
GtMatchIteratorSW *mis;
GtSeq *seq_a, *seq_b;
char *a, *b;
const char *adesc, *bdesc;
GtAlignment *ali = NULL;
unsigned long seqlen_a, seqlen_b, seqpos;
GtRange arng, brng;
gt_assert(mi && match);
mis = gt_match_iterator_sw_cast(mi);
while (true) {
if (!mis->pvt->firstali)
mis->pvt->seqno_es2++;
if (mis->pvt->seqno_es2 == gt_encseq_num_of_sequences(mis->pvt->es2)) {
mis->pvt->seqno_es1++;
if (mis->pvt->seqno_es1 == gt_encseq_num_of_sequences(mis->pvt->es1))
return GT_MATCHER_STATUS_END;
mis->pvt->seqno_es2 = 0;
}
seqlen_a = gt_encseq_seqlength(mis->pvt->es1, mis->pvt->seqno_es1);
seqlen_b = gt_encseq_seqlength(mis->pvt->es2, mis->pvt->seqno_es2);
/* XXX: reuse buffers for performance improvement */
a = gt_malloc(seqlen_a * sizeof (char));
seqpos = gt_encseq_seqstartpos(mis->pvt->es1, mis->pvt->seqno_es1);
gt_encseq_extract_decoded(mis->pvt->es1, a, seqpos, seqpos + seqlen_a - 1);
b = gt_malloc(seqlen_b * sizeof (char));
seqpos = gt_encseq_seqstartpos(mis->pvt->es2, mis->pvt->seqno_es2);
gt_encseq_extract_decoded(mis->pvt->es1, b, seqpos, seqpos + seqlen_b - 1);
seq_a = gt_seq_new(a, seqlen_a, gt_encseq_alphabet(mis->pvt->es1));
seq_b = gt_seq_new(b, seqlen_b, gt_encseq_alphabet(mis->pvt->es2));
ali = gt_swalign(seq_a, seq_b, mis->pvt->sf);
mis->pvt->firstali = false;
if (ali && gt_alignment_get_length(ali) >= mis->pvt->min_len
&& gt_alignment_eval(ali) <= mis->pvt->max_edist) {
break;
}
gt_alignment_delete(ali);
gt_seq_delete(seq_a);
gt_seq_delete(seq_b);
gt_free(a);
gt_free(b);
}
arng = gt_alignment_get_urange(ali);
brng = gt_alignment_get_vrange(ali);
adesc = gt_encseq_description(mis->pvt->es1, &seqlen_a, mis->pvt->seqno_es1);
bdesc = gt_encseq_description(mis->pvt->es2, &seqlen_b, mis->pvt->seqno_es2);
*match = gt_match_sw_new("", "",
mis->pvt->seqno_es1,
mis->pvt->seqno_es2,
gt_alignment_get_length(ali),
gt_alignment_eval(ali),
arng.start, brng.start,
arng.end, brng.end,
GT_MATCH_DIRECT);
gt_match_set_seqid1_nt(*match, adesc, seqlen_a);
gt_match_set_seqid2_nt(*match, bdesc, seqlen_b);
gt_alignment_delete(ali);
gt_seq_delete(seq_a);
gt_seq_delete(seq_b);
gt_free(a);
gt_free(b);
return GT_MATCHER_STATUS_OK;
}
