static void pbs_attach_results_to_gff3(GtPBSResults *results,
GtLTRElement *element,
GtStrand *canonical_strand,
GtStr *tag)
{
GtRange pbs_range;
GtGenomeNode *gf;
unsigned long i = 0;
char buffer[BUFSIZ];
GtPBSHit* hit = gt_pbs_results_get_ranked_hit(results, i++);
if (*canonical_strand == GT_STRAND_UNKNOWN)
*canonical_strand = gt_pbs_hit_get_strand(hit);
else
{
/* do we have to satisfy a strand constraint?
* then find best-scoring PBS on the given canonical strand */
while (gt_pbs_hit_get_strand(hit) != *canonical_strand
&& i < gt_pbs_results_get_number_of_hits(results))
{
gt_log_log("dropping PBS because of nonconsistent strand: %s\n",
gt_feature_node_get_attribute(element->mainnode, "ID"));
hit = gt_pbs_results_get_ranked_hit(results, i++);
}
/* if there is none, do not report a PBS */
if (gt_pbs_hit_get_strand(hit) != *canonical_strand)
return;
}
pbs_range = gt_pbs_hit_get_coords(hit);
pbs_range.start++; pbs_range.end++; /* GFF3 is 1-based */
gf = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*)
element->mainnode),
GT_PBS_TYPE,
pbs_range.start,
pbs_range.end,
gt_pbs_hit_get_strand(hit));
gt_feature_node_set_source((GtFeatureNode*) gf, tag);
gt_feature_node_set_score((GtFeatureNode*) gf,
(float) gt_pbs_hit_get_score(hit));
if (gt_pbs_hit_get_trna(hit) != NULL) {
gt_feature_node_add_attribute((GtFeatureNode*) gf, "trna",
gt_pbs_hit_get_trna(hit));
}
gt_feature_node_set_strand(element->mainnode, gt_pbs_hit_get_strand(hit));
(void) snprintf(buffer, BUFSIZ-1, "%lu", gt_pbs_hit_get_tstart(hit));
gt_feature_node_add_attribute((GtFeatureNode*) gf, "trnaoffset", buffer);
(void) snprintf(buffer, BUFSIZ-1, "%lu", gt_pbs_hit_get_offset(hit));
gt_feature_node_add_attribute((GtFeatureNode*) gf, "pbsoffset", buffer);
(void) snprintf(buffer, BUFSIZ-1, "%lu", gt_pbs_hit_get_edist(hit));
gt_feature_node_add_attribute((GtFeatureNode*) gf, "edist", buffer);
gt_feature_node_add_child(element->mainnode, (GtFeatureNode*) gf);
}
int gt_pbs_unit_test(GtError *err)
{
int had_err = 0;
GtLTRElement element;
GtPBSOptions o;
GtStr *tmpfilename;
FILE *tmpfp;
GtPBSResults *res;
GtPBSHit *hit;
double score1, score2;
GtRange rng;
char *rev_seq,
*seq,
tmp[BUFSIZ];
const char *fullseq = "aaaaaaaaaaaaaaaaaaaa"
"tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
"tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
"acatactaggatgctag" /* <- PBS forward */
"aatatagtttcgaatatagcactgcatttcgaa"
"tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
"tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
"tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
"tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
"tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
"tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
"tatagcactgcatttcgaatatagtttcgaatatag"
/* PBS reverse -> */ "gatcctaaggctac"
"tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
"tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
"aaaaaaaaaaaaaaaaaaaa";
/* notice previous errors */
gt_error_check(err);
/* create temporary tRNA library file */
tmpfilename = gt_str_new();
tmpfp = gt_xtmpfp(tmpfilename);
fprintf(tmpfp, ">test1\nccccccccccccccctagcatcctagtatgtccc\n"
">test2\ncccccccccgatcctagggctaccctttc\n");
gt_fa_xfclose(tmpfp);
ensure(had_err, gt_file_exists(gt_str_get(tmpfilename)));
/* setup testing parameters */
o.radius = 30;
o.max_edist = 1;
o.alilen.start = 11;
o.alilen.end = 30;
o.offsetlen.start = 0;
o.offsetlen.end = 5;
o.trnaoffsetlen.start = 0;
o.trnaoffsetlen.end = 40;
o.ali_score_match = 5;
o.ali_score_mismatch = -10;
o.ali_score_insertion = o.ali_score_deletion = -20;
o.trna_lib = gt_bioseq_new(gt_str_get(tmpfilename), err);
ensure(had_err, gt_bioseq_number_of_sequences(o.trna_lib) == 2);
element.leftLTR_5 = 20;
element.leftLTR_3 = 119;
element.rightLTR_5 = 520;
element.rightLTR_3 = 619;
/* setup sequences */
seq = gt_malloc(600 * sizeof (char));
rev_seq = gt_malloc(600 * sizeof (char));
memcpy(seq, fullseq + 20, 600);
memcpy(rev_seq, fullseq + 20, 600);
gt_reverse_complement(rev_seq, 600, err);
/* try to find PBS in sequences */
res = gt_pbs_find(seq, rev_seq, &element, &o, err);
ensure(had_err, res != NULL);
ensure(had_err, gt_pbs_results_get_number_of_hits(res) == 2);
/* check first hit on forward strand */
hit = gt_pbs_results_get_ranked_hit(res, 0);
ensure(had_err, hit != NULL);
ensure(had_err, gt_pbs_hit_get_alignment_length(hit) == 17);
ensure(had_err, gt_pbs_hit_get_edist(hit) == 0);
ensure(had_err, gt_pbs_hit_get_offset(hit) == 0);
ensure(had_err, gt_pbs_hit_get_tstart(hit) == 3);
ensure(had_err, strcmp(gt_pbs_hit_get_trna(hit), "test1") == 0);
rng = gt_pbs_hit_get_coords(hit);
ensure(had_err, rng.start == 120);
ensure(had_err, rng.end == 136);
score1 = gt_pbs_hit_get_score(hit);
ensure(had_err, gt_pbs_hit_get_strand(hit) == GT_STRAND_FORWARD);
memset(tmp, 0, BUFSIZ-1);
memcpy(tmp, fullseq + (rng.start * sizeof (char)),
(rng.end - rng.start + 1) * sizeof (char));
ensure(had_err, strcmp(tmp, "acatactaggatgctag" ) == 0);
/* check second hit on reverse strand */
hit = gt_pbs_results_get_ranked_hit(res, 1);
ensure(had_err, hit != NULL);
ensure(had_err, gt_pbs_hit_get_alignment_length(hit) == 14);
ensure(had_err, gt_pbs_hit_get_edist(hit) == 1);
ensure(had_err, gt_pbs_hit_get_offset(hit) == 0);
ensure(had_err, gt_pbs_hit_get_tstart(hit) == 6);
ensure(had_err, strcmp(gt_pbs_hit_get_trna(hit), "test2") == 0);
rng = gt_pbs_hit_get_coords(hit);
ensure(had_err, rng.start == 506);
ensure(had_err, rng.end == 519);
score2 = gt_pbs_hit_get_score(hit);
ensure(had_err, gt_double_compare(score1, score2) > 0);
ensure(had_err, gt_pbs_hit_get_strand(hit) == GT_STRAND_REVERSE);
memset(tmp, 0, BUFSIZ-1);
memcpy(tmp, fullseq + (rng.start * sizeof (char)),
(rng.end - rng.start + 1) * sizeof (char));
ensure(had_err, strcmp(tmp, "gatcctaaggctac" ) == 0);
/* clean up */
gt_xremove(gt_str_get(tmpfilename));
ensure(had_err, !gt_file_exists(gt_str_get(tmpfilename)));
gt_str_delete(tmpfilename);
gt_bioseq_delete(o.trna_lib);
gt_free(rev_seq);
gt_free(seq);
gt_pbs_results_delete(res);
return had_err;
}
