int splicing_exonset_init(splicing_exonset_t *ex, size_t size) {
SPLICING_CHECK(splicing_strvector_init(&ex->seqids, 0));
SPLICING_FINALLY(splicing_strvector_destroy, &ex->seqids);
SPLICING_CHECK(splicing_vector_int_init(&ex->seqid, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &ex->seqid);
SPLICING_CHECK(splicing_vector_int_init(&ex->start, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &ex->start);
SPLICING_CHECK(splicing_vector_int_init(&ex->end, 0));
SPLICING_FINALLY(splicing_vector_int_destroy, &ex->end);
SPLICING_FINALLY_CLEAN(4);
return 0;
}
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);
}
int pysplicing_to_strvector(PyObject *pv, splicing_strvector_t *v) {
int i, n;
if (!PyTuple_Check(pv)) {
PyErr_SetString(PyExc_TypeError, "Need a tuple");
return 1;
}
n=PyTuple_Size(pv);
splicing_strvector_init(v, 0);
splicing_strvector_reserve(v, n);
for (i=0; i<n; i++) {
PyObject *it=PyTuple_GetItem(pv, i);
splicing_strvector_append(v,PyString_AsString(it));
}
return 0;
}
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);
}