int splicing_gff_exon_start_end(const splicing_gff_t *gff,
splicing_vector_int_t *start,
splicing_vector_int_t *end,
splicing_vector_int_t *idx,
int gene) {
size_t noiso;
int i=0, p=0, n=splicing_gff_size(gff);
int pos;
size_t nogenes;
splicing_vector_int_t tmp, tmp2;
SPLICING_CHECK(splicing_vector_int_init(&tmp, 10));
SPLICING_FINALLY(splicing_vector_int_destroy, &tmp);
SPLICING_CHECK(splicing_vector_int_init(&tmp2, 10));
SPLICING_FINALLY(splicing_vector_int_destroy, &tmp2);
SPLICING_CHECK(splicing_gff_nogenes(gff, &nogenes));
if (gene < 0 || gene >= nogenes) {
SPLICING_ERROR("Invalid gene id", SPLICING_EINVAL);
}
pos=VECTOR(gff->genes)[gene]+1;
SPLICING_CHECK(splicing_gff_noiso_one(gff, gene, &noiso));
splicing_vector_int_clear(start);
splicing_vector_int_clear(end);
SPLICING_CHECK(splicing_vector_int_resize(idx, noiso+1));
while (pos < n) {
if (VECTOR(gff->type)[pos] == SPLICING_TYPE_EXON) {
int s=VECTOR(gff->start)[pos];
int e=VECTOR(gff->end)[pos];
SPLICING_CHECK(splicing_vector_int_push_back(start, s)); p++;
SPLICING_CHECK(splicing_vector_int_push_back(end, e));
} else if (VECTOR(gff->type)[pos] == SPLICING_TYPE_MRNA) {
VECTOR(*idx)[i] = p;
if (i!=0) {
SPLICING_CHECK(splicing_i_gff_exon_start_end_sort(start, end, idx,
i-1, &tmp, &tmp2));
}
i++;
} else if (VECTOR(gff->type)[pos] == SPLICING_TYPE_GENE) {
break;
}
pos++;
}
VECTOR(*idx)[i] = p;
SPLICING_CHECK(splicing_i_gff_exon_start_end_sort(start, end, idx, i-1,
&tmp, &tmp2));
splicing_vector_int_destroy(&tmp2);
splicing_vector_int_destroy(&tmp);
SPLICING_FINALLY_CLEAN(1);
return 0;
}
int splicing_gff_converter_init(const splicing_gff_t *gff, size_t gene,
splicing_gff_converter_t *converter) {
int i;
SPLICING_CHECK(splicing_gff_noiso_one(gff, gene, &converter->noiso));
SPLICING_VECTOR_INT_INIT_FINALLY(&converter->exstart, 0);
SPLICING_VECTOR_INT_INIT_FINALLY(&converter->exend, 0);
SPLICING_VECTOR_INT_INIT_FINALLY(&converter->exidx, 0);
SPLICING_VECTOR_INT_INIT_FINALLY(&converter->shift, 0);
SPLICING_VECTOR_INT_INIT_FINALLY(&converter->exlim, 0);
SPLICING_CHECK(splicing_gff_exon_start_end(gff, &converter->exstart,
&converter->exend,
&converter->exidx, gene));
/* Calculate the shift */
for (i=0; i < converter->noiso; i++) {
size_t cs=0, ce=0, ex=0;
int pos=VECTOR(converter->exidx)[i], pos2=VECTOR(converter->exidx)[i+1];
while (pos < pos2) {
cs += VECTOR(converter->exstart)[pos];
SPLICING_CHECK(splicing_vector_int_push_back(&converter->shift,
cs-ce-ex-1));
ex++; ce += VECTOR(converter->exend)[pos]; pos++;
}
}
/* Calculate the exlim */
for (i=0; i < converter->noiso; i++) {
size_t cs=0;
int pos=VECTOR(converter->exidx)[i], pos2=VECTOR(converter->exidx)[i+1];
while (pos < pos2) {
size_t l=
VECTOR(converter->exend)[pos] - VECTOR(converter->exstart)[pos]+1;
cs += l;
SPLICING_CHECK(splicing_vector_int_push_back(&converter->exlim, cs+1));
pos++;
}
}
SPLICING_FINALLY_CLEAN(5);
return 0;
}
int splicing_exonset_append(splicing_exonset_t *ex, const char *seqid,
int start, int end) {
size_t idx;
int seen=splicing_strvector_search(&ex->seqids, seqid, &idx);
if (seen) {
SPLICING_CHECK(splicing_vector_int_push_back(&ex->seqid, idx));
} else {
size_t size=splicing_strvector_size(&ex->seqids);
SPLICING_CHECK(splicing_strvector_append(&ex->seqids, seqid));
SPLICING_CHECK(splicing_vector_int_push_back(&ex->seqid, size));
}
SPLICING_CHECK(splicing_vector_int_push_back(&ex->start, start));
SPLICING_CHECK(splicing_vector_int_push_back(&ex->end, end));
return 0;
}
int splicing_genomic_to_iso(const splicing_gff_t *gff, size_t gene,
const splicing_vector_int_t *position,
splicing_matrix_int_t *isopos) {
size_t r, i, noiso, noreads=splicing_vector_int_size(position);
splicing_vector_int_t exstart, exend, exidx, shift;
splicing_gff_noiso_one(gff, gene, &noiso);
SPLICING_CHECK(splicing_vector_int_init(&exstart, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &exstart);
SPLICING_CHECK(splicing_vector_int_init(&exend, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &exend);
SPLICING_CHECK(splicing_vector_int_init(&exidx, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &exidx);
SPLICING_CHECK(splicing_gff_exon_start_end(gff, &exstart, &exend,
&exidx, gene));
SPLICING_CHECK(splicing_vector_int_init(&shift, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &shift);
for (i=0; i<noiso; i++) {
size_t cs=0, ce=0, ex=0;
int pos=VECTOR(exidx)[i], pos2=VECTOR(exidx)[i+1];
while (pos < pos2) {
cs += VECTOR(exstart)[pos];
SPLICING_CHECK(splicing_vector_int_push_back(&shift, cs-ce-ex-1));
ex++; ce += VECTOR(exend)[pos]; pos++;
}
}
SPLICING_CHECK(splicing_matrix_int_resize(isopos, noiso, noreads));
for (r=0; r<noreads; r++) {
for (i=0; i<noiso; i++) {
size_t pos=VECTOR(*position)[r];
size_t startpos=VECTOR(exidx)[i];
size_t endpos=VECTOR(exidx)[i+1];
int ex;
for (ex=startpos; ex < endpos && VECTOR(exend)[ex] < pos; ex++) ;
if (VECTOR(exstart)[ex] <= pos && pos <= VECTOR(exend)[ex]) {
MATRIX(*isopos, i, r) = VECTOR(*position)[r] - VECTOR(shift)[ex];
} else {
MATRIX(*isopos, i, r) = -1;
}
}
}
splicing_vector_int_destroy(&shift);
splicing_vector_int_destroy(&exidx);
splicing_vector_int_destroy(&exend);
splicing_vector_int_destroy(&exstart);
SPLICING_FINALLY_CLEAN(4);
return 0;
}
int splicing_gff_append(splicing_gff_t *gff, const char *seqid,
const char *source, splicing_type_t type, int start,
int end, double score, splicing_strand_t strand,
int phase, const char *ID, const char *parent) {
if (type == SPLICING_TYPE_GENE) {
gff->nogenes++;
SPLICING_CHECK(splicing_vector_int_push_back(&gff->genes, gff->n));
SPLICING_CHECK(splicing_vector_int_push_back(&gff->strand, strand));
} else if (type == SPLICING_TYPE_MRNA) {
gff->notranscripts++;
SPLICING_CHECK(splicing_vector_int_push_back(&gff->transcripts, gff->n));
}
if (type == SPLICING_TYPE_GENE) {
/* Seqid */
if (!strcmp(seqid, gff->last_seqid)) {
int last=splicing_vector_int_tail(&gff->seqid);
SPLICING_CHECK(splicing_vector_int_push_back(&gff->seqid, last));
} else {
size_t idx;
int seen=splicing_strvector_search(&gff->seqids, seqid, &idx);
if (seen) {
SPLICING_CHECK(splicing_vector_int_push_back(&gff->seqid, idx));
gff->last_seqid=splicing_strvector_get(&gff->seqids, idx);
} else {
size_t size=splicing_strvector_size(&gff->seqids);
SPLICING_CHECK(splicing_strvector_append(&gff->seqids, seqid));
SPLICING_CHECK(splicing_vector_int_push_back(&gff->seqid, size));
gff->last_source=splicing_strvector_get(&gff->seqids, size);
}
}
/* Source */
if (!strcmp(source, gff->last_source)) {
int last=splicing_vector_int_tail(&gff->source);
SPLICING_CHECK(splicing_vector_int_push_back(&gff->source, last));
} else {
size_t idx;
int seen=splicing_strvector_search(&gff->sources, source, &idx);
if (seen) {
SPLICING_CHECK(splicing_vector_int_push_back(&gff->source, idx));
gff->last_source=splicing_strvector_get(&gff->sources, idx);
} else {
size_t size=splicing_strvector_size(&gff->sources);
SPLICING_CHECK(splicing_strvector_append(&gff->sources, source));
SPLICING_CHECK(splicing_vector_int_push_back(&gff->source, size));
gff->last_source=splicing_strvector_get(&gff->sources, size);
}
}
}
/* Parent */
if (!parent || !parent[0]) {
SPLICING_CHECK(splicing_vector_int_push_back(&gff->parent, -1));
} else if (!strcmp(parent, gff->last_gene_id)) {
SPLICING_CHECK(splicing_vector_int_push_back(&gff->parent,
gff->last_gene_no));
} else if (!strcmp(parent, gff->last_mrna_id)) {
SPLICING_CHECK(splicing_vector_int_push_back(&gff->parent,
gff->last_mrna_no));
} else {
size_t idx;
int seen=splicing_strvector_search(&gff->ID, parent, &idx);
if (!seen) {
SPLICING_WARNING("Unknown parent ID, invalid GFF file");
SPLICING_CHECK(splicing_vector_int_push_back(&gff->parent, -1));
} else {
SPLICING_CHECK(splicing_vector_int_push_back(&gff->parent, idx));
}
}
SPLICING_CHECK(splicing_vector_int_push_back(&gff->type, type));
SPLICING_CHECK(splicing_vector_int_push_back(&gff->start, start));
SPLICING_CHECK(splicing_vector_int_push_back(&gff->end, end));
SPLICING_CHECK(splicing_vector_push_back(&gff->score, score));
SPLICING_CHECK(splicing_vector_int_push_back(&gff->phase, phase));
SPLICING_CHECK(splicing_strvector_append(&gff->ID, ID));
/* Update last gene/mrna */
if (type == SPLICING_TYPE_GENE) {
gff->last_gene_id = splicing_strvector_get(&gff->ID, gff->n);
gff->last_gene_no = gff->n;
} else if (type == SPLICING_TYPE_MRNA) {
gff->last_mrna_id = splicing_strvector_get(&gff->ID, gff->n);
gff->last_mrna_no = gff->n;
}
gff->n += 1;
return 0;
}
int splicing_iso_to_genomic(const splicing_gff_t *gff, size_t gene,
const splicing_vector_int_t *isoform,
const splicing_vector_int_t *exstart,
const splicing_vector_int_t *exend,
const splicing_vector_int_t *exidx,
splicing_vector_int_t *position) {
size_t i, noiso, n=splicing_vector_int_size(position);
splicing_vector_int_t exlim, shift;
splicing_vector_int_t vexstart, vexend, vexidx,
*myexstart=(splicing_vector_int_t *) exstart,
*myexend=(splicing_vector_int_t *) exend,
*myexidx=(splicing_vector_int_t *) exidx;
size_t pos, pos2;
if (!exstart || !exend || !exidx) {
myexstart=&vexstart;
myexend=&vexend;
myexidx=&vexidx;
SPLICING_CHECK(splicing_vector_int_init(myexstart, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, myexstart);
SPLICING_CHECK(splicing_vector_int_init(myexend, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, myexend);
SPLICING_CHECK(splicing_vector_int_init(myexidx, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, myexidx);
SPLICING_CHECK(splicing_gff_exon_start_end(gff, myexstart, myexend,
myexidx, gene));
}
SPLICING_CHECK(splicing_gff_noiso_one(gff, gene, &noiso));
SPLICING_CHECK(splicing_vector_int_init(&exlim, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &exlim);
SPLICING_CHECK(splicing_vector_int_init(&shift, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &shift);
for (i=0; i<noiso; i++) {
size_t cs=0, ce=0, ex=0;
int pos=VECTOR(*myexidx)[i], pos2=VECTOR(*myexidx)[i+1];
while (pos < pos2) {
cs += VECTOR(*myexstart)[pos];
SPLICING_CHECK(splicing_vector_int_push_back(&shift, cs-ce-ex-1));
ex++; ce += VECTOR(*myexend)[pos]; pos++;
}
}
for (i=0; i<noiso; i++) {
size_t cs=0;
int pos=VECTOR(*myexidx)[i], pos2=VECTOR(*myexidx)[i+1];
while (pos < pos2) {
size_t l=VECTOR(*myexend)[pos]-VECTOR(*myexstart)[pos]+1;
cs += l;
SPLICING_CHECK(splicing_vector_int_push_back(&exlim, cs+1));
pos++;
}
}
for (i=0; i<n; i++) {
int iso=VECTOR(*isoform)[i];
size_t pos=VECTOR(*position)[i];
int ex;
for (ex=VECTOR(*myexidx)[iso]; VECTOR(exlim)[ex] <= pos; ex++) ;
VECTOR(*position)[i] = pos + VECTOR(shift)[ex];
}
splicing_vector_int_destroy(&shift);
splicing_vector_int_destroy(&exlim);
SPLICING_FINALLY_CLEAN(2);
if (!exstart || !exend || !exidx) {
splicing_vector_int_destroy(myexidx);
splicing_vector_int_destroy(myexend);
splicing_vector_int_destroy(myexstart);
SPLICING_FINALLY_CLEAN(3);
}
return 0;
}
