Ejemplo n.º 1
0
Archivo: gff.c Proyecto: mlovci/MISO
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);
}
Ejemplo n.º 2
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);
}
Ejemplo n.º 3
0
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);
}
Ejemplo n.º 4
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);
}
Ejemplo n.º 5
0
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);
}
Ejemplo n.º 6
0
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);
}