int splicing_dgesdd(const splicing_matrix_t *matrix,
splicing_vector_t *values) {
splicing_matrix_t tmp;
int m=splicing_matrix_nrow(matrix);
int n=splicing_matrix_ncol(matrix);
int lda=m, minmn= m < n ? m : n, maxmn = m < n ? n : m;
int lwork=-1;
int info=0;
splicing_vector_t work;
splicing_vector_int_t iwork;
char jobz='N';
int dummy=1;
double dummy2;
SPLICING_CHECK(splicing_matrix_copy(&tmp, matrix));
SPLICING_FINALLY(splicing_matrix_destroy, &tmp);
SPLICING_CHECK(splicing_vector_init(&work, 1));
SPLICING_FINALLY(splicing_vector_destroy, &work);
SPLICING_CHECK(splicing_vector_int_init(&iwork, 8*minmn));
SPLICING_FINALLY(splicing_vector_int_destroy, &iwork);
SPLICING_CHECK(splicing_vector_resize(values, minmn));
/* Get the optiomal lwork first*/
splicingdgesdd_(&jobz, &m, &n, &MATRIX(tmp,0,0), &lda, VECTOR(*values),
/*U=*/ &dummy2, /*LDU=*/ &dummy,
/*VT=*/ &dummy2, /*LDVT=*/ &dummy,
VECTOR(work), &lwork, VECTOR(iwork), &info);
lwork = VECTOR(work)[0];
SPLICING_CHECK(splicing_vector_resize(&work, lwork));
/* Now do the SVD */
splicingdgesdd_(&jobz, &m, &n, &MATRIX(tmp,0,0), &lda, VECTOR(*values),
/*U=*/ &dummy2, /*LDU=*/ &dummy,
/*VT=*/ &dummy2, /*LDVT=*/ &dummy,
VECTOR(work), &lwork, VECTOR(iwork), &info);
if (info != 0) {
SPLICING_ERROR("Cannot calculate SVD", SPLICING_ELAPACK);
}
splicing_vector_destroy(&work);
splicing_vector_int_destroy(&iwork);
splicing_matrix_destroy(&tmp);
SPLICING_FINALLY_CLEAN(3);
return 0;
}
int splicing_io_get_string(FILE *input, char *buffer, size_t maxlen,
size_t *len, char delim, int newline) {
int c;
*len = 0;
while (1) {
c=fgetc(input);
if (c==EOF) {
SPLICING_ERROR("Invalid GFF file", SPLICING_PARSEERROR);
} else if (*len == maxlen) {
SPLICING_ERROR("Invalid GFF file", SPLICING_PARSEERROR);
} else if (c==delim) {
*buffer='\0';
buffer++;
return 0;
} else if (newline && (c=='\n' || c=='\r')) {
*buffer='\0';
buffer++;
return 0;
} else if (!newline && (c=='\n' || c=='\r')) {
SPLICING_ERROR("Invalid GFF file", SPLICING_PARSEERROR);
} else {
*buffer=(char) c;
buffer++;
*len += 1;
}
}
return 1;
}
int splicing_io_get_real_na(FILE *input, double *real, char delim,
char nachar) {
char buffer[30];
char *bufend;
size_t len;
double na=SPLICING_NA_REAL;
int eof = splicing_io_get_string(input, buffer,
sizeof(buffer)/sizeof(char), &len,
delim, /*newline=*/ 0);
if (eof) {
SPLICING_ERROR("Invalid GFF file", SPLICING_PARSEERROR);
}
if (len > 0 && buffer[0]==nachar) {
*real=na;
return 0;
}
*real = strtod(buffer, &bufend);
if (*bufend != '\0') {
SPLICING_ERROR("Invalid GFF file", SPLICING_PARSEERROR);
}
return 0;
}
int splicing_io_get_integer_na(FILE *input, int *integer, char delim,
char nachar) {
char buffer[30];
char *bufend;
size_t len;
int na=SPLICING_NA_INTEGER;
int eof = splicing_io_get_string(input, buffer,
sizeof(buffer)/sizeof(char), &len,
delim, /*newline=*/ 0);
if (eof) {
SPLICING_ERROR("Invalid GFF file", SPLICING_PARSEERROR);
}
if (len > 0 && buffer[0]==nachar) {
*integer=na;
return 0;
}
*integer = (int) strtol(buffer, &bufend, /*base=*/ 10);
if (*bufend != '\0') {
SPLICING_ERROR("Invalid GFF file", SPLICING_PARSEERROR);
}
return 0;
}
int splicing_io_parse_attributes(char *attr, char **ID, char**parent) {
*ID=SPLICING_STRVECTOR_ZERO; *parent=SPLICING_STRVECTOR_ZERO;
char *kw, *vl;
while (*attr != '\0') {
/* Skip white space */
while (*attr != '\0' && isspace(*attr)) {
attr++;
}
/* Keyword */
kw=attr;
while (*attr != '\0' && *attr != '=') {
attr++;
}
if (*attr == '\0') {
SPLICING_ERROR("Invalid GFF file", SPLICING_PARSEERROR);
}
*attr='\0'; attr++;
/* Value */
vl=attr;
while (*attr != '\0' && *attr != ';') {
attr++;
}
if (*attr == ';') { *attr='\0'; attr++; }
if (!strcmp("ID", kw)) {
*ID=vl;
} else if (!strcmp("Parent", kw)) {
*parent=vl;
}
}
return 0;
}
int splicing_gff_noexons_one(const splicing_gff_t *gff, size_t gene,
splicing_vector_int_t *noexons) {
size_t nogenes, idx1, idx2, noiso, pos, il;
SPLICING_CHECK(splicing_gff_nogenes(gff, &nogenes));
if (gene >= nogenes) {
SPLICING_ERROR("Invalid gene id", SPLICING_EINVAL);
}
idx1=VECTOR(gff->genes)[gene];
idx2= gene+1 == nogenes ? gff->n : VECTOR(gff->genes)[gene+1];
for (noiso=0; idx1 < idx2; idx1++) {
if (VECTOR(gff->type)[idx1] == SPLICING_TYPE_MRNA) { noiso += 1; }
}
SPLICING_CHECK(splicing_vector_int_resize(noexons, noiso));
idx1=VECTOR(gff->genes)[gene];
idx2= gene+1 == nogenes ? gff->n : VECTOR(gff->genes)[gene+1];
for (; idx1 < idx2 && VECTOR(gff->type)[idx1] != SPLICING_TYPE_MRNA;
idx1++) ;
idx1++;
for (pos=0, il=0; idx1 < idx2; idx1++) {
if (VECTOR(gff->type)[idx1] == SPLICING_TYPE_MRNA) {
VECTOR(*noexons)[pos++]=il;
il=0;
} else if (VECTOR(gff->type)[idx1] == SPLICING_TYPE_EXON) { il++; }
}
VECTOR(*noexons)[pos++]=il;
return 0;
}
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;
}
/* TODO: do not ignore size */
int splicing_gff_init(splicing_gff_t *gff, size_t size) {
if (size < 0) {
SPLICING_ERROR("Cannot create GFF, `size' must be non-negative",
SPLICING_EINVAL);
}
SPLICING_CHECK(splicing_strvector_init(&gff->seqids, 0));
SPLICING_FINALLY(splicing_strvector_destroy, &gff->seqids);
SPLICING_CHECK(splicing_strvector_init(&gff->sources, 0));
SPLICING_FINALLY(splicing_strvector_destroy, &gff->sources);
SPLICING_CHECK(splicing_strvector_init(&gff->ID, 0));
SPLICING_FINALLY(splicing_strvector_destroy, &gff->ID);
SPLICING_CHECK(splicing_vector_int_init(&gff->genes, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &gff->genes);
SPLICING_CHECK(splicing_vector_int_init(&gff->transcripts, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &gff->transcripts);
SPLICING_CHECK(splicing_vector_int_init(&gff->seqid, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &gff->seqid);
SPLICING_CHECK(splicing_vector_int_init(&gff->source, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &gff->source);
SPLICING_CHECK(splicing_vector_int_init(&gff->strand, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &gff->strand);
SPLICING_CHECK(splicing_vector_int_init(&gff->type, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &gff->type);
SPLICING_CHECK(splicing_vector_int_init(&gff->start, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &gff->start);
SPLICING_CHECK(splicing_vector_int_init(&gff->end, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &gff->end);
SPLICING_CHECK(splicing_vector_init(&gff->score, 0));
SPLICING_FINALLY(splicing_vector_destroy, &gff->score);
SPLICING_CHECK(splicing_vector_int_init(&gff->phase, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &gff->phase);
SPLICING_CHECK(splicing_vector_int_init(&gff->parent, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &gff->parent);
gff->n=0;
gff->nogenes=0;
gff->notranscripts=0;
gff->last_gene_id = gff->last_mrna_id = SPLICING_STRVECTOR_ZERO;
gff->last_gene_no = gff->last_mrna_no = -1;
gff->last_seqid = gff->last_source = SPLICING_STRVECTOR_ZERO;
SPLICING_FINALLY_CLEAN(14);
return 0;
}
int splicing_gff_gene_start_end_one(const splicing_gff_t *gff, size_t gene,
size_t *start, size_t *end) {
size_t nogenes=splicing_vector_int_size(&gff->genes);
size_t idx;
if (gene < 0 || gene >= nogenes) {
SPLICING_ERROR("Invalid gene id", SPLICING_EINVAL);
}
idx=VECTOR(gff->genes)[gene];
*start=VECTOR(gff->start)[idx];
*end=VECTOR(gff->end)[idx];
return 0;
}
int splicing_gff_constitutive_exons(const splicing_gff_t *gff,
splicing_exonset_t *exons,
int min_length,
splicing_constitutive_mode_t mode) {
switch (mode) {
case SPLICING_CONSTITUTIVE_ALL:
return splicing_i_gff_constitutive_exons_all(gff, exons, min_length);
break;
case SPLICING_CONSTITUTIVE_FULL:
return splicing_i_gff_constitutive_exons_full(gff, exons, min_length);
break;
default:
SPLICING_ERROR("Unknown `mode' argument for constitutive exon finding",
SPLICING_EINVAL);
}
}
int splicing_i_gff_reindex_cmp(void *data, const void *a, const void *b) {
splicing_gff_t *gff=(splicing_gff_t *) data;
int aa=*(int*)a, bb=*(int*)b;
int parent_a=VECTOR(gff->parent)[aa];
int parent_b=VECTOR(gff->parent)[bb];
int gparent_a= parent_a == -1 ? -1 : VECTOR(gff->parent)[parent_a];
int gparent_b= parent_b == -1 ? -1 : VECTOR(gff->parent)[parent_b];
const char *a_gene_id, *b_gene_id, *a_mrna_id, *b_mrna_id;
int c1, c2;
/* If gene ids differ */
a_gene_id = gparent_a != -1 ? STR(gparent_a) :
(parent_a != -1 ? STR(parent_a) : STR(aa));
b_gene_id = gparent_b != -1 ? STR(gparent_b) :
(parent_b != -1 ? STR(parent_b) : STR(bb));
c1=strcmp(a_gene_id, b_gene_id); if (c1 != 0) { return c1; }
/* Or if mRNA ids differ */
a_mrna_id = gparent_a != -1 ? STR(parent_a) : STR(aa);
b_mrna_id = gparent_b != -1 ? STR(parent_b) : STR(bb);
c2=strcmp(a_mrna_id, b_mrna_id); if (c2 != 0) { return c2; }
/* Otherwise gene first, then mRNA, then the rest according to
start position */
if (parent_a == -1 && parent_b != -1) {
return -1;
} else if (parent_a != -1 && parent_b == -1) {
return 1;
} else if (gparent_a == -1 && gparent_b != -1) {
return -1;
} else if (gparent_a != -1 && gparent_b == -1) {
return 1;
} else if (gparent_a != -1 && gparent_b != -1) {
int sa=VECTOR(gff->start)[aa];
int sb=VECTOR(gff->start)[bb];
if (sa < sb) { return -1; } else if (sa > sb) { return 1; }
return 0;
} else {
SPLICING_ERROR("Invalid GFF file, cannot order records",
SPLICING_EINVAL);
}
return 0;
}
int splicing_iso_to_genomic_all(const splicing_gff_t *gff, size_t gene,
int position,
const splicing_gff_converter_t *converter,
splicing_vector_int_t *result) {
size_t i;
splicing_gff_converter_t vconverter,
*myconverter = (splicing_gff_converter_t*) converter;
if (position < 1) {
SPLICING_ERROR("Invalid isoform coordinate, must the larger than zero",
SPLICING_EINVAL);
}
if (!converter) {
myconverter=&vconverter;
SPLICING_CHECK(splicing_gff_converter_init(gff, gene, myconverter));
SPLICING_FINALLY(splicing_gff_converter_destroy, myconverter);
}
SPLICING_CHECK(splicing_vector_int_resize(result, myconverter->noiso));
/* TODO: find impossible positions */
for (i=0; i<myconverter->noiso; i++) {
int ex;
for (ex=VECTOR(myconverter->exidx)[i];
ex < VECTOR(myconverter->exidx)[i+1] &&
VECTOR(myconverter->exlim)[ex] <= position;
ex++) ;
if (ex < VECTOR(myconverter->exidx)[i+1]) {
VECTOR(*result)[i] = position + VECTOR(myconverter->shift)[ex];
} else {
VECTOR(*result)[i] = -1;
}
}
if (!converter) {
splicing_gff_converter_destroy(myconverter);
SPLICING_FINALLY_CLEAN(1);
}
return 0;
}
int splicing_i_gff_noiso_one(const splicing_gff_t *gff, size_t gene,
size_t *noiso, splicing_vector_int_t *isolen) {
size_t nogenes, idx1, idx2;
SPLICING_CHECK(splicing_gff_nogenes(gff, &nogenes));
if (gene < 0 || gene >= nogenes) {
SPLICING_ERROR("Invalid gene id", SPLICING_EINVAL);
}
idx1=VECTOR(gff->genes)[gene];
idx2= gene+1 == nogenes ? gff->n : VECTOR(gff->genes)[gene+1];
*noiso = 0;
for ( ; idx1 < idx2; idx1++) {
if (VECTOR(gff->type)[idx1] == SPLICING_TYPE_MRNA) { *noiso += 1; }
}
if (isolen) {
size_t il=0, pos=0;
SPLICING_CHECK(splicing_vector_int_resize(isolen, *noiso));
idx1=VECTOR(gff->genes)[gene];
idx2= gene+1 == nogenes ? gff->n : VECTOR(gff->genes)[gene+1];
for (; idx1 < idx2 && VECTOR(gff->type)[idx1] != SPLICING_TYPE_MRNA;
idx1++) ;
idx1++;
for (; idx1 < idx2; idx1++) {
if (VECTOR(gff->type)[idx1] == SPLICING_TYPE_MRNA) {
VECTOR(*isolen)[pos++]=il;
il = 0;
} else if (VECTOR(gff->type)[idx1] == SPLICING_TYPE_EXON) {
il += VECTOR(gff->end)[idx1] - VECTOR(gff->start)[idx1] + 1;
}
}
VECTOR(*isolen)[pos++]=il;
}
return 0;
}
int splicing_gff_fprint_gene(const splicing_gff_t *gff,
FILE *outfile, int gene) {
size_t nogenes, noiso;
int i, j;
splicing_vector_int_t start, end, idx;
SPLICING_CHECK(splicing_gff_nogenes(gff, &nogenes));
if (gene < 0 || gene >= nogenes) {
SPLICING_ERROR("Invalid gene ID", SPLICING_EINVAL);
}
SPLICING_CHECK(splicing_vector_int_init(&start, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &start);
SPLICING_CHECK(splicing_vector_int_init(&end, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &end);
SPLICING_CHECK(splicing_vector_int_init(&idx, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &idx);
SPLICING_CHECK(splicing_gff_exon_start_end(gff, &start, &end, &idx, gene));
noiso = splicing_vector_int_size(&idx)-1;
fprintf(outfile, "===\nGene with %i isoforms:\n", (int) noiso);
for (i=0; i<noiso; i++) {
fprintf(outfile, " Isoform %i:\n", i);
for (j=VECTOR(idx)[i]; j<VECTOR(idx)[i+1]; j++) {
fprintf(outfile, " %i-%i\n", VECTOR(start)[j], VECTOR(end)[j]);
}
}
splicing_vector_int_destroy(&idx);
splicing_vector_int_destroy(&end);
splicing_vector_int_destroy(&start);
SPLICING_FINALLY_CLEAN(3);
return 0;
}
int splicing_miso_trinity(const splicing_matrix_t *match_matrix,
const splicing_vector_int_t *isolen,
int readLength, int noIterations, int noBurnIn,
int noLag, const splicing_vector_t *hyperp,
splicing_matrix_t *samples,
splicing_vector_t *logLik,
splicing_matrix_t *class_templates,
splicing_vector_t *class_counts,
splicing_vector_int_t *assignment,
splicing_miso_rundata_t *rundata) {
double acceptP, cJS, pJS, sigma;
int noiso = splicing_matrix_nrow(match_matrix);
int noReads = splicing_matrix_ncol(match_matrix);
splicing_vector_int_t *myass=assignment, vass;
splicing_vector_t vpsi, vpsiNew, valpha, valphaNew,
*psi=&vpsi, *psiNew=&vpsiNew, *alpha=&valpha, *alphaNew=&valphaNew;
int noSamples = (noIterations - noBurnIn + 1) / noLag;
int i, m, lagCounter=0, noS=0;
splicing_vector_int_t match_order;
splicing_vector_int_t effisolen;
splicing_vector_t isoscores;
if ( (class_templates ? 1 : 0) + (class_counts ? 1 : 0) == 1) {
SPLICING_ERROR("Only one of `class_templates' and `class_counts' is "
"given", SPLICING_EINVAL);
}
rundata->noIso=noiso;
rundata->noIters=noIterations;
rundata->noBurnIn=noBurnIn;
rundata->noLag=noLag;
rundata->noAccepted = rundata->noRejected = 0;
if (assignment) {
SPLICING_CHECK(splicing_vector_int_resize(myass, noReads));
splicing_vector_int_null(myass);
} else {
myass=&vass;
SPLICING_CHECK(splicing_vector_int_init(myass, noReads));
SPLICING_FINALLY(splicing_vector_int_destroy, myass);
}
SPLICING_CHECK(splicing_vector_init(&vpsi, noiso));
SPLICING_FINALLY(splicing_vector_destroy, &vpsi);
SPLICING_CHECK(splicing_vector_init(&vpsiNew, noiso));
SPLICING_FINALLY(splicing_vector_destroy, &vpsiNew);
SPLICING_CHECK(splicing_vector_init(&valpha, noiso-1));
SPLICING_FINALLY(splicing_vector_destroy, &valpha);
SPLICING_CHECK(splicing_vector_init(&valphaNew, noiso-1));
SPLICING_FINALLY(splicing_vector_destroy, &valphaNew);
SPLICING_CHECK(splicing_vector_int_init(&match_order, noReads));
SPLICING_FINALLY(splicing_vector_int_destroy, &match_order);
SPLICING_CHECK(splicing_order_matches(match_matrix, &match_order));
if (class_templates && class_counts) {
SPLICING_CHECK(splicing_i_miso_classes(match_matrix, &match_order,
class_templates, class_counts,
/*bin_class_templates=*/ 0,
/*bin_class_counts=*/ 0));
}
SPLICING_CHECK(splicing_vector_int_init(&effisolen, noiso));
SPLICING_FINALLY(splicing_vector_int_destroy, &effisolen);
SPLICING_CHECK(splicing_vector_init(&isoscores, noiso));
SPLICING_FINALLY(splicing_vector_destroy, &isoscores);
for (i=0; i<noiso; i++) {
int l=VECTOR(*isolen)[i]-readLength+1;
VECTOR(effisolen)[i] = l > 0 ? l : 0;
VECTOR(isoscores)[i] = -log((double) l);
}
SPLICING_CHECK(splicing_matrix_resize(samples, noiso, noSamples));
SPLICING_CHECK(splicing_vector_resize(logLik, noSamples));
/* Initialize Psi(0) randomly */
SPLICING_CHECK(splicing_drift_proposal(/* mode= */ 0, 0, 0, 0, 0, 0,
noiso, psi, alpha, &sigma, 0));
SPLICING_CHECK(splicing_drift_proposal(/* mode= */ 1, psi, alpha, sigma,
0, 0, noiso, psi, alpha, 0, 0));
/* Initialize assignments of reads */
SPLICING_CHECK(splicing_reassign_samples(match_matrix, &match_order, psi,
noiso, myass));
/* foreach Iteration m=1, ..., M do */
for (m=0; m < noIterations; m++) {
SPLICING_CHECK(splicing_drift_proposal(/* mode= */ 1, psi, alpha, sigma,
0, 0, noiso, psiNew, alphaNew, 0,
0));
SPLICING_CHECK(splicing_metropolis_hastings_ratio(myass, noReads, psiNew,
alphaNew, psi, alpha,
sigma, noiso,
&effisolen, hyperp,
&isoscores,
m > 0 ? 1 : 0,
&acceptP, &cJS, &pJS));
if (acceptP >= 1 || RNG_UNIF01() < acceptP) {
splicing_vector_t *tmp;
tmp=psi; psi=psiNew; psiNew=tmp;
tmp=alpha; alpha=alphaNew; alphaNew=tmp;
cJS = pJS;
rundata->noAccepted ++;
} else {
rundata->noRejected ++;
}
if (m >= noBurnIn) {
if (lagCounter == noLag - 1) {
memcpy(&MATRIX(*samples, 0, noS), VECTOR(*psi),
noiso * sizeof(double));
VECTOR(*logLik)[noS] = cJS;
noS++;
lagCounter = 0;
} else {
lagCounter ++;
}
}
SPLICING_CHECK(splicing_reassign_samples(match_matrix, &match_order,
psi, noiso, myass));
} /* for m < noIterations */
splicing_vector_destroy(&isoscores);
splicing_vector_int_destroy(&effisolen);
splicing_vector_int_destroy(&match_order);
splicing_vector_destroy(&valphaNew);
splicing_vector_destroy(&valpha);
splicing_vector_destroy(&vpsiNew);
splicing_vector_destroy(&vpsi);
SPLICING_FINALLY_CLEAN(7);
if (!assignment) {
splicing_vector_int_destroy(myass);
SPLICING_FINALLY_CLEAN(1);
}
return 0;
}
int splicing_simulate_paired_reads(const splicing_gff_t *gff, int gene,
const splicing_vector_t *expression,
int noreads, int readLength,
const splicing_vector_t *fragmentProb,
int fragmentStart, double normalMean,
double normalVar, double numDevs,
splicing_vector_int_t *isoform,
splicing_vector_int_t *position,
splicing_strvector_t *cigar,
splicing_vector_t *sampleprob) {
size_t i, j, noiso, il, nogenes;
splicing_vector_t *mysampleprob=sampleprob, vsampleprob;
splicing_vector_t px, cpx;
double sumpx, sumpsi=0.0;
splicing_vector_int_t isolen;
int goodiso=0;
splicing_vector_int_t exstart, exend, exidx;
splicing_vector_t *myfragmentProb=(splicing_vector_t*) fragmentProb,
vfragmentProb;
int fs, fl;
SPLICING_CHECK(splicing_gff_nogenes(gff, &nogenes));
if (gene < 0 || gene >= nogenes) {
SPLICING_ERROR("Invalid gene id", SPLICING_EINVAL);
}
/* TODO: more error checks */
if (!fragmentProb) {
myfragmentProb=&vfragmentProb;
SPLICING_CHECK(splicing_vector_init(&vfragmentProb, 0));
SPLICING_FINALLY(splicing_vector_destroy, &vfragmentProb);
SPLICING_CHECK(splicing_normal_fragment(normalMean, normalVar, numDevs,
readLength, myfragmentProb,
&fragmentStart));
splicing_vector_scale(myfragmentProb,
1.0/splicing_vector_sum(myfragmentProb));
}
il=splicing_vector_size(myfragmentProb);
fs=fragmentStart;
fl=fragmentStart+il-1;
SPLICING_CHECK(splicing_gff_noiso_one(gff, gene, &noiso));
if ( fabs(splicing_vector_sum(myfragmentProb) - 1.0) > 1e-10 ) {
SPLICING_ERROR("Fragment length distribution does not sum up to 1",
SPLICING_EINVAL);
}
SPLICING_CHECK(splicing_vector_int_init(&isolen, noiso));
SPLICING_FINALLY(splicing_vector_int_destroy, &isolen);
SPLICING_CHECK(splicing_gff_isolength_one(gff, gene, &isolen));
SPLICING_CHECK(splicing_vector_copy(&px, myfragmentProb));
SPLICING_FINALLY(splicing_vector_destroy, &px);
SPLICING_CHECK(splicing_vector_init(&cpx, il));
SPLICING_FINALLY(splicing_vector_destroy, &cpx);
if (!sampleprob) {
mysampleprob=&vsampleprob;
SPLICING_CHECK(splicing_vector_init(mysampleprob, noiso));
SPLICING_FINALLY(splicing_vector_destroy, mysampleprob);
} else {
SPLICING_CHECK(splicing_vector_resize(mysampleprob, noiso));
}
for (sumpx=VECTOR(px)[0], i=1; i<il; i++) {
VECTOR(px)[i] += VECTOR(px)[i-1];
sumpx += VECTOR(px)[i];
}
VECTOR(cpx)[0] = VECTOR(px)[0];
for (i=1; i<il; i++) {
VECTOR(cpx)[i] = VECTOR(cpx)[i-1] + VECTOR(px)[i];
}
for (i=0; i<noiso; i++) {
int ilen=VECTOR(isolen)[i];
int r1= ilen >= fl ? ilen - fl + 1 : 0;
int r2= ilen >= fs ? (ilen >= fl ? fl - fs : ilen - fs + 1) : 0;
/* int r3= fs - 1; */
double sp=0.0;
if (r1 > 0) { sp += r1; }
if (r2 > 0) { sp += VECTOR(cpx)[r2-1]; }
VECTOR(*mysampleprob)[i] = sp * VECTOR(*expression)[i];
if (VECTOR(*mysampleprob)[i] != 0) { goodiso += 1; }
sumpsi += VECTOR(*mysampleprob)[i];
}
if (goodiso == 0) {
SPLICING_ERROR("No isoform is possible", SPLICING_FAILURE);
}
for (i=1; i<noiso; i++) {
VECTOR(*mysampleprob)[i] += VECTOR(*mysampleprob)[i-1];
}
SPLICING_CHECK(splicing_vector_int_resize(isoform, noreads*2));
for (i=0; i<2*noreads; i+=2) {
int w;
double rand;
if (noiso==1) {
w=0;
} else if (noiso==2) {
rand = RNG_UNIF01() * sumpsi;
w = (rand < VECTOR(*mysampleprob)[0]) ? 0 : 1;
} else {
rand = RNG_UNIF01() * sumpsi;
for (w=0; rand > VECTOR(*mysampleprob)[w]; w++) ;
}
VECTOR(*isoform)[i]=VECTOR(*isoform)[i+1]=w;
}
if (!sampleprob) {
splicing_vector_destroy(mysampleprob);
SPLICING_FINALLY_CLEAN(1);
} else {
for (i=noiso-1; i>0; i--) {
VECTOR(*mysampleprob)[i] -= VECTOR(*mysampleprob)[i-1];
}
}
/* We have the isoforms, now get the read positions. */
SPLICING_CHECK(splicing_vector_int_resize(position, noreads*2));
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));
/* Positions in isoform coordinates first.
These are sampled based on the fragment length distribution. */
for (i=0, j=0; i<noreads; i++) {
int iso=VECTOR(*isoform)[2*i];
int ilen=VECTOR(isolen)[iso];
int r1= ilen >= fl ? ilen - fl + 1 : 0;
int r2= ilen >= fs ? (ilen >= fl ? fl - fs : ilen - fs + 1) : 0;
/* int r3= fs - 1; */
int pos, fragment;
double sp=0.0;
if (r1 > 0) { sp += r1; }
if (r2 > 0) { sp += VECTOR(cpx)[r2-1]; }
double rand=RNG_UNIF(0, sp);
if (rand < r1) {
pos = ceil(rand);
} else {
int w;
rand -= r1;
for (w=0; VECTOR(cpx)[w] < rand; w++) ;
pos = r1 + r2 - w;
}
if (pos <= r1) {
rand=RNG_UNIF(0, 1.0);
} else {
rand=RNG_UNIF(0, VECTOR(px)[r1+r2-pos]);
}
for (fragment=0; VECTOR(px)[fragment] < rand; fragment++) ;
fragment += fragmentStart;
VECTOR(*position)[j++] = pos;
VECTOR(*position)[j++] = pos+fragment-readLength;
}
/* Translate positions to genomic coordinates */
/* TODO: some of this is already calculated */
SPLICING_CHECK(splicing_iso_to_genomic(gff, gene, isoform, /*converter=*/ 0,
position));
/* CIGAR strings */
splicing_strvector_clear(cigar);
SPLICING_CHECK(splicing_strvector_reserve(cigar, 2*noreads));
for (j=0; j<2*noreads; j++) {
char tmp[1000], *tmp2=tmp;
int iso=VECTOR(*isoform)[j];
size_t rs=VECTOR(*position)[j];
int ex=0;
int rl=readLength;
for (ex=VECTOR(exidx)[iso]; VECTOR(exend)[ex] < rs; ex++) ;
while (rs + rl - 1 > VECTOR(exend)[ex]) {
tmp2 += snprintf(tmp2, sizeof(tmp)/sizeof(char)-(tmp2-tmp)-1, "%iM%iN",
(int) (VECTOR(exend)[ex]-rs+1),
(int) (VECTOR(exstart)[ex+1]-VECTOR(exend)[ex]-1));
if (tmp2 >= tmp + sizeof(tmp)/sizeof(char)) {
SPLICING_ERROR("CIGAR string too long", SPLICING_EINVAL);
}
rl -= (VECTOR(exend)[ex] - rs + 1);
rs = VECTOR(exstart)[ex+1];
ex++;
}
tmp2 += snprintf(tmp2, sizeof(tmp)/sizeof(char)-(tmp2-tmp)-1, "%iM", rl);
if (tmp2 >= tmp + sizeof(tmp)/sizeof(char)) {
SPLICING_ERROR("CIGAR string too long", SPLICING_EINVAL);
}
SPLICING_CHECK(splicing_strvector_append(cigar, tmp));
}
splicing_vector_int_destroy(&exidx);
splicing_vector_int_destroy(&exend);
splicing_vector_int_destroy(&exstart);
splicing_vector_destroy(&cpx);
splicing_vector_destroy(&px);
splicing_vector_int_destroy(&isolen);
SPLICING_FINALLY_CLEAN(6);
if (!fragmentProb) {
splicing_vector_destroy(myfragmentProb);
SPLICING_FINALLY_CLEAN(1);
}
return 0;
}
int splicing_gff_read(FILE *input, splicing_gff_t *gff) {
int eof=!EOF;
char seqid[200];
char source[200];
char type[200];
int start, end, phase;
double score;
char strand[10];
char attributes[5000];
size_t len;
splicing_type_t realtype;
splicing_strand_t realstrand=SPLICING_STRAND_UNKNOWN;
char *ID, *parent;
do {
eof = eof || splicing_io_skip_newline_and_comments(input);
eof = eof || splicing_io_get_string(input, seqid,
sizeof(seqid)/sizeof(char), &len,
/*delim=*/ '\t', /*newline=*/ 0);
eof = eof || splicing_io_get_string(input, source,
sizeof(source)/sizeof(char), &len,
/*delim=*/ '\t', /*newline=*/ 0);
eof = eof || splicing_io_get_string(input, type,
sizeof(type)/sizeof(char), &len,
/*delim=*/ '\t', /*newline=*/ 0);
eof = eof || splicing_io_get_integer(input, &start, /*delim=*/ '\t');
eof = eof || splicing_io_get_integer(input, &end, /*delim=*/ '\t');
eof = eof || splicing_io_get_real_na(input, &score, /*delim=*/ '\t',
/*nachar=*/ '.');
eof = eof || splicing_io_get_string(input, strand,
sizeof(strand)/sizeof(char), &len,
/*delim=*/ '\t', /*newline=*/ 0);
eof = eof || splicing_io_get_integer_na(input, &phase, /*delim=*/ '\t',
/*nachar=*/ '.');
eof = eof || splicing_io_get_string(input, attributes,
sizeof(attributes)/sizeof(char), &len,
/*delim=*/ '\n', /*newline=*/ 1);
if (eof) {
SPLICING_ERROR("Corrupt GFF file", SPLICING_PARSEERROR);
}
/* TODO: do not hardcode these names
TODO: order them according to their frequency */
if (!strcmp(type, "gene")) {
realtype = SPLICING_TYPE_GENE;
} else if (!strcmp(type, "mRNA")) {
realtype = SPLICING_TYPE_MRNA;
} else if (!strcmp(type, "exon")) {
realtype = SPLICING_TYPE_EXON;
} else if (!strcmp(type, "CDS")) {
realtype = SPLICING_TYPE_CDS;
} else if (!strcmp(type, "start_codon")) {
realtype = SPLICING_TYPE_START_CODON;
} else if (!strcmp(type, "stop_codon")) {
realtype = SPLICING_TYPE_STOP_CODON;
} else {
SPLICING_ERROR("Invalid GFF file", SPLICING_PARSEERROR);
}
if (!strcmp(strand, "+")) {
realstrand=SPLICING_STRAND_PLUS;
} else if (!strcmp(strand, "-")) {
realstrand=SPLICING_STRAND_MINUS;
} else if (!strcmp(strand, ".")) {
realstrand=SPLICING_STRAND_UNKNOWN;
}
/* Parsing the attributes field */
SPLICING_CHECK(splicing_io_parse_attributes(attributes, &ID, &parent));
SPLICING_CHECK(splicing_gff_append(gff, seqid, source, realtype, start,
end, score, realstrand, phase, ID,
parent));
eof = splicing_io_skip_newline_and_comments(input);
} while (!eof);
return 0;
}
int splicing_simulate_reads(const splicing_gff_t *gff, int gene,
const splicing_vector_t *expression,
int noreads, int readLength,
splicing_vector_int_t *isoform,
splicing_vector_int_t *position,
splicing_strvector_t *cigar,
splicing_vector_t *sample_prob) {
size_t i, p, noiso, goodiso=0, nogenes;
splicing_vector_int_t effisolen;
splicing_vector_t sampleprob;
double rand, sumpsi=0.0;
splicing_vector_int_t exstart, exend, exidx;
SPLICING_CHECK(splicing_gff_nogenes(gff, &nogenes));
if (gene < 0 || gene >= nogenes) {
SPLICING_ERROR("Invalid gene id", SPLICING_EINVAL);
}
/* TODO: more error checks */
SPLICING_CHECK(splicing_gff_noiso_one(gff, gene, &noiso));
SPLICING_CHECK(splicing_vector_int_init(&effisolen, noiso));
SPLICING_FINALLY(splicing_vector_int_destroy, &effisolen);
SPLICING_CHECK(splicing_vector_init(&sampleprob, noiso));
SPLICING_FINALLY(splicing_vector_destroy, &sampleprob);
SPLICING_CHECK(splicing_vector_int_resize(isoform, noreads));
SPLICING_CHECK(splicing_gff_isolength_one(gff, gene, &effisolen));
for (i=0; i<noiso; i++) {
int l=VECTOR(effisolen)[i]-readLength+1;
VECTOR(effisolen)[i] = l > 0 ? l : 0;
VECTOR(sampleprob)[i] = VECTOR(*expression)[i] * VECTOR(effisolen)[i];
if (VECTOR(sampleprob)[i] != 0) { goodiso++; }
sumpsi += VECTOR(sampleprob)[i];
}
if (goodiso==0) {
SPLICING_ERROR("No isoform is possible", SPLICING_FAILURE);
}
if (sample_prob) {
SPLICING_CHECK(splicing_vector_update(sample_prob, &sampleprob));
}
for (i=1; i<noiso; i++) {
VECTOR(sampleprob)[i] += VECTOR(sampleprob)[i-1];
}
for (i=0; i<noreads; i++) {
int w;
if (noiso==1) {
w=0;
} else if (noiso==2) {
rand = RNG_UNIF01() * sumpsi;
w = (rand < VECTOR(sampleprob)[0]) ? 0 : 1;
} else {
rand = RNG_UNIF01() * sumpsi;
for (w=0; rand > VECTOR(sampleprob)[w]; w++) ;
}
VECTOR(*isoform)[i]=w;
}
splicing_vector_destroy(&sampleprob);
SPLICING_FINALLY_CLEAN(1);
/* OK, we have the isoforms, now we need the read positions,
these are uniformly sampled from the individual isoforms. */
SPLICING_CHECK(splicing_vector_int_resize(position, noreads));
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));
/* Positions in isoform coordinates first */
for (i=0; i<noreads; i++) {
int iso=VECTOR(*isoform)[i];
int len=VECTOR(effisolen)[iso];
VECTOR(*position)[i]=RNG_INTEGER(1, len);
}
/* Translate isoform coordinates to genomic coordintes */
/* TODO: some of this is already calculated */
SPLICING_CHECK(splicing_iso_to_genomic(gff, gene, isoform, /*converter=*/ 0,
position));
/* CIGAR strings */
splicing_strvector_clear(cigar);
SPLICING_CHECK(splicing_strvector_reserve(cigar, noreads));
for (i=0; i<noreads; i++) {
char tmp[1000], *tmp2=tmp;
int iso=VECTOR(*isoform)[i];
size_t rs=VECTOR(*position)[i];
int ex=0;
int rl=readLength;
for (ex=VECTOR(exidx)[iso]; VECTOR(exend)[ex] < rs; ex++) ;
while (VECTOR(exend)[ex] < rs+rl-1) {
tmp2 += snprintf(tmp2, sizeof(tmp)/sizeof(char)-(tmp2-tmp)-1, "%iM%iN",
(int) (VECTOR(exend)[ex]-rs+1),
(int) (VECTOR(exstart)[ex+1]-VECTOR(exend)[ex]-1));
if (tmp2 >= tmp + sizeof(tmp)/sizeof(char)) {
SPLICING_ERROR("CIGAR string too long", SPLICING_EINVAL);
}
rl -= (VECTOR(exend)[ex] - rs + 1);
rs = VECTOR(exstart)[ex+1];
ex++;
}
tmp2 += snprintf(tmp2, sizeof(tmp)/sizeof(char)-(tmp2-tmp)-1, "%iM", rl);
if (tmp2 >= tmp + sizeof(tmp)/sizeof(char)) {
SPLICING_ERROR("CIGAR string too long", SPLICING_EINVAL); }
SPLICING_CHECK(splicing_strvector_append(cigar, tmp));
}
splicing_vector_int_destroy(&exidx);
splicing_vector_int_destroy(&exend);
splicing_vector_int_destroy(&exstart);
splicing_vector_int_destroy(&effisolen);
SPLICING_FINALLY_CLEAN(4);
return 0;
}
int splicing_gene_complexity(const splicing_gff_t *gff, size_t gene,
int readLength, splicing_complexity_t type,
splicing_norm_t norm, int paired,
const splicing_vector_t *fragmentProb,
int fragmentStart, double normalMean,
double normalVar, double numDevs,
double *complexity) {
splicing_matrix_t assignment_matrix;
SPLICING_CHECK(splicing_matrix_init(&assignment_matrix, 0, 0));
SPLICING_FINALLY(splicing_matrix_destroy, &assignment_matrix);
if (!paired) {
SPLICING_CHECK(splicing_assignment_matrix(gff, gene, readLength,
&assignment_matrix));
} else {
SPLICING_CHECK(splicing_paired_assignment_matrix(gff, gene, readLength,
fragmentProb,
fragmentStart,
normalMean, normalVar,
numDevs,
&assignment_matrix));
}
switch (type) {
case SPLICING_COMPLEXITY_RELATIVE:
switch (norm) {
splicing_vector_t values;
int i, n;
case SPLICING_NORM_2:
SPLICING_CHECK(splicing_vector_init(&values, 0));
SPLICING_FINALLY(splicing_vector_destroy, &values);
SPLICING_CHECK(splicing_dgesdd(&assignment_matrix, &values));
n=splicing_vector_size(&values);
for (i=n-1; i>=0 && VECTOR(values)[i] < 1e-14; i--) ;
*complexity = VECTOR(values)[0] / VECTOR(values)[i];
splicing_vector_destroy(&values);
SPLICING_FINALLY_CLEAN(1);
break;
case SPLICING_NORM_1:
SPLICING_ERROR("One norm not implemented", SPLICING_UNIMPLEMENTED);
break;
case SPLICING_NORM_INFINITY:
SPLICING_ERROR("Infinity norm not implemented", SPLICING_UNIMPLEMENTED);
break;
}
break;
case SPLICING_COMPLEXITY_ABSOLUTE:
SPLICING_ERROR("Absolute complexity not implemented",
SPLICING_UNIMPLEMENTED);
break;
}
splicing_matrix_destroy(&assignment_matrix);
SPLICING_FINALLY_CLEAN(1);
return 0;
}
