void splicing_gff_destroy(splicing_gff_t *gff) {
splicing_strvector_destroy(&gff->seqids);
splicing_strvector_destroy(&gff->sources);
splicing_strvector_destroy(&gff->ID);
splicing_vector_int_destroy(&gff->genes);
splicing_vector_int_destroy(&gff->transcripts);
splicing_vector_int_destroy(&gff->seqid);
splicing_vector_int_destroy(&gff->source);
splicing_vector_int_destroy(&gff->strand);
splicing_vector_int_destroy(&gff->type);
splicing_vector_int_destroy(&gff->start);
splicing_vector_int_destroy(&gff->end);
splicing_vector_destroy(&gff->score);
splicing_vector_int_destroy(&gff->phase);
splicing_vector_int_destroy(&gff->parent);
}
static PyObject* pysplicing_simulate_paired_reads(PyObject *self,
PyObject *args) {
PyObject *gff, *expression;
int gene, noreads, readlength;
double normalMean, normalVar, numDevs;
splicing_gff_t *mygff;
splicing_vector_t myexpression;
splicing_vector_int_t isoform, position;
splicing_strvector_t cigar;
PyObject *r1, *r2, *r3;
if (!PyArg_ParseTuple(args, "OiOiiddd", &gff, &gene, &expression,
&noreads, &readlength, &normalMean, &normalVar,
&numDevs)) { return NULL; }
mygff=PyCObject_AsVoidPtr(gff);
if (pysplicing_to_vector(expression, &myexpression)) { return NULL; }
SPLICING_FINALLY(splicing_vector_destroy, &myexpression);
SPLICING_PYCHECK(splicing_vector_int_init(&isoform, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &isoform);
SPLICING_PYCHECK(splicing_vector_int_init(&position, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &position);
SPLICING_PYCHECK(splicing_strvector_init(&cigar, 0));
SPLICING_FINALLY(splicing_strvector_destroy, &cigar);
SPLICING_PYCHECK(splicing_simulate_paired_reads(mygff, gene, &myexpression,
noreads, readlength,
/*insertProb=*/ 0,
/*insertStart=*/ 0,
normalMean, normalVar,
numDevs, &isoform,
&position, &cigar, 0));
r1=pysplicing_from_vector_int(&isoform);
r2=pysplicing_from_vector_int(&position);
r3=pysplicing_from_strvector(&cigar);
splicing_strvector_destroy(&cigar);
splicing_vector_int_destroy(&position);
splicing_vector_int_destroy(&isoform);
splicing_vector_destroy(&myexpression);
SPLICING_FINALLY_CLEAN(4);
return Py_BuildValue("OOO", r1, r2, r3);
}
static PyObject* pysplicing_solve_gene(PyObject *self, PyObject *args) {
PyObject *gff, *readcigar, *position;
int gene, readLength;
splicing_gff_t *mygff;
splicing_vector_int_t myposition;
splicing_strvector_t myreadcigar;
splicing_matrix_t match_matrix, assignment_matrix;
splicing_vector_t expression;
PyObject *r1, *r2, *r3;
if (!PyArg_ParseTuple(args, "OiiOO", &gff, &gene, &readLength, &position,
&readcigar)) { return NULL; }
mygff=PyCObject_AsVoidPtr(gff);
if (pysplicing_to_vector_int(position, &myposition)) { return NULL; }
SPLICING_FINALLY(splicing_vector_int_destroy, &myposition);
if (pysplicing_to_strvector(readcigar, &myreadcigar)) { return NULL; }
SPLICING_FINALLY(splicing_strvector_destroy, &myreadcigar);
SPLICING_PYCHECK(splicing_matrix_init(&match_matrix, 0, 0));
SPLICING_FINALLY(splicing_matrix_destroy, &match_matrix);
SPLICING_PYCHECK(splicing_matrix_init(&assignment_matrix, 0, 0));
SPLICING_FINALLY(splicing_matrix_destroy, &assignment_matrix);
SPLICING_PYCHECK(splicing_vector_init(&expression, 0));
SPLICING_FINALLY(splicing_vector_destroy, &expression);
SPLICING_PYCHECK(splicing_solve_gene(mygff, gene, readLength, &myposition,
(const char **) myreadcigar.table,
&match_matrix, &assignment_matrix,
&expression));
r1=pysplicing_from_matrix(&match_matrix);
r2=pysplicing_from_matrix(&assignment_matrix);
r3=pysplicing_from_vector(&expression);
splicing_vector_destroy(&expression);
splicing_matrix_destroy(&assignment_matrix);
splicing_matrix_destroy(&match_matrix);
splicing_strvector_destroy(&myreadcigar);
splicing_vector_int_destroy(&myposition);
SPLICING_FINALLY_CLEAN(5);
return Py_BuildValue("OOO", r1, r2, r3);
}
static PyObject* pysplicing_simulate_reads(PyObject *self, PyObject *args) {
PyObject *gff, *expression;
int gene, noreads, readLength;
splicing_vector_t myexpression;
splicing_gff_t *mygff;
splicing_vector_int_t isoform, position;
splicing_strvector_t cigar;
PyObject *risoform, *rposition, *rcigar;
if (!PyArg_ParseTuple(args, "OiOii", &gff, &gene, &expression, &noreads,
&readLength)) { return NULL; }
mygff=PyCObject_AsVoidPtr(gff);
if (pysplicing_to_vector(expression, &myexpression)) { return NULL; }
SPLICING_FINALLY(splicing_vector_destroy, &myexpression);
SPLICING_PYCHECK(splicing_strvector_init(&cigar, 0));
SPLICING_FINALLY(splicing_strvector_destroy, &cigar);
SPLICING_PYCHECK(splicing_vector_int_init(&position, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &position);
SPLICING_PYCHECK(splicing_vector_int_init(&isoform, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &isoform);
SPLICING_PYCHECK(splicing_simulate_reads(mygff, gene, &myexpression,
noreads, readLength,
&isoform, &position, &cigar));
risoform = pysplicing_from_vector_int(&isoform);
splicing_vector_int_destroy(&isoform);
SPLICING_FINALLY_CLEAN(1);
rposition = pysplicing_from_vector_int(&position);
splicing_vector_int_destroy(&position);
SPLICING_FINALLY_CLEAN(1);
rcigar = pysplicing_from_strvector(&cigar);
splicing_strvector_destroy(&cigar);
SPLICING_FINALLY_CLEAN(1);
splicing_vector_destroy(&myexpression);
SPLICING_FINALLY_CLEAN(1);
return Py_BuildValue("OOO", risoform, rposition, rcigar);
}
static PyObject* pysplicing_miso(PyObject *self, PyObject *args) {
PyObject *gff, *readpos, *readcigar, *hyperp=0;
int gene, readLength, noIterations=5000, noBurnIn=500, noLag=10;
splicing_gff_t *mygff;
splicing_strvector_t myreadcigar;
splicing_vector_int_t myreadpos;
splicing_vector_t myhyperp;
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;
PyObject *r1, *r2, *r3, *r4, *r5, *r6;
if (!PyArg_ParseTuple(args, "OiOOi|iiiO", &gff, &gene, &readpos, &readcigar,
&readLength, &noIterations, &noBurnIn, &noLag,
&hyperp)) { return NULL; }
mygff=PyCObject_AsVoidPtr(gff);
SPLICING_PYCHECK(splicing_matrix_init(&samples, 0, 0));
SPLICING_FINALLY(splicing_matrix_destroy, &samples);
SPLICING_PYCHECK(splicing_vector_init(&logLik, 0));
SPLICING_FINALLY(splicing_vector_destroy, &logLik);
SPLICING_PYCHECK(splicing_matrix_init(&class_templates, 0, 0));
SPLICING_FINALLY(splicing_matrix_destroy, &class_templates);
SPLICING_PYCHECK(splicing_vector_init(&class_counts, 0));
SPLICING_FINALLY(splicing_vector_destroy, &class_counts);
SPLICING_PYCHECK(splicing_vector_int_init(&assignment, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &assignment);
if (pysplicing_to_vector_int(readpos, &myreadpos)) { return NULL; }
SPLICING_FINALLY(splicing_vector_int_destroy, &myreadpos);
if (hyperp) {
if (pysplicing_to_vector(hyperp, &myhyperp)) { return NULL; }
SPLICING_FINALLY(splicing_vector_destroy, &myhyperp);
} else {
size_t i, noiso;
SPLICING_PYCHECK(splicing_gff_noiso_one(mygff, gene, &noiso));
SPLICING_PYCHECK(splicing_vector_init(&myhyperp, noiso));
SPLICING_FINALLY(splicing_vector_destroy, &myhyperp);
for (i=0; i<noiso; i++) { VECTOR(myhyperp)[i] = 1.0; }
}
if (pysplicing_to_strvector(readcigar, &myreadcigar)) { return NULL; };
SPLICING_FINALLY(splicing_strvector_destroy, &myreadcigar);
SPLICING_PYCHECK(splicing_miso(mygff, gene, &myreadpos,
(const char**) myreadcigar.table,
readLength, noIterations, noBurnIn, noLag,
&myhyperp, &samples, &logLik,
/*match_matrix=*/ 0, &class_templates,
&class_counts, &assignment, &rundata));
splicing_vector_destroy(&myhyperp);
splicing_vector_int_destroy(&myreadpos);
splicing_strvector_destroy(&myreadcigar);
SPLICING_FINALLY_CLEAN(3);
r6=pysplicing_from_miso_rundata(&rundata);
r5=pysplicing_from_vector_int(&assignment);
splicing_vector_int_destroy(&assignment); SPLICING_FINALLY_CLEAN(1);
r4=pysplicing_from_vector(&class_counts);
splicing_vector_destroy(&class_counts); SPLICING_FINALLY_CLEAN(1);
splicing_matrix_transpose(&class_templates);
r3=pysplicing_from_matrix(&class_templates);
splicing_matrix_destroy(&class_templates); SPLICING_FINALLY_CLEAN(1);
r2=pysplicing_from_vector(&logLik);
splicing_vector_destroy(&logLik); SPLICING_FINALLY_CLEAN(1);
r1=pysplicing_from_matrix(&samples);
splicing_matrix_destroy(&samples); SPLICING_FINALLY_CLEAN(1);
return Py_BuildValue("OOOOOO", r1, r2, r3, r4, r5, r6);
}
void splicing_exonset_destroy(splicing_exonset_t *ex) {
splicing_strvector_destroy(&ex->seqids);
splicing_vector_int_destroy(&ex->seqid);
splicing_vector_int_destroy(&ex->start);
splicing_vector_int_destroy(&ex->end);
}