def __handle_all_duos(self, request):
'''Similar to __FamilyParentChildPhaser, only works with parent-child duos and does not compare
multiple children in a family. Handles all duos; processes children in pre-ordering (top-to-bottom
in the pedigree).'''
problem, params = request.problem, request.params
# Build all duos
duos = np.empty((0, 3), dtype=int)
for parent_type in constants.ALLELES:
d = problem.duos(parent_type)
duos = np.concatenate((duos,
np.concatenate(
(d, np.tile(parent_type, (d.shape[0], 1))),
axis=1)))
# Pre-order nodes
duos = duos[np.argsort([problem.pedigree.depth[x] for x in duos[:, 0]]), :]
h = problem.haplotype
for child, parent, parent_type in duos:
ibd.phase_by_ibd(
problem,
ip.ibd_segments_in_duo(
h,
parent,
child,
parent_type,
parent_het_fill_threshold=params.het_fill_threshold,
debug=params.debug),
'max',
debug=params.debug)
return False
def __handle_outer_duos(self, request):
'''Similar to __FamilyParentChildPhaser, only works with parent-child duos and does not compare
multiple children in a family. Handles only children outside nuclear families.'''
problem, params = request.problem, request.params
h = problem.haplotype
family_members = problem.families_union(min_children=0)
for parent_type in constants.ALLELES:
for child, parent in pt.selected_duos(problem, params, parent_type):
if not util.is_member(family_members, [child]):
ibd.phase_by_ibd(request, ip.ibd_segments_in_duo(h, parent, child, parent_type,
parent_het_fill_threshold=params.het_fill_threshold,
debug=params.debug), 'max')
return False
def __handle_outer_duos(self, request):
'''Similar to __FamilyParentChildPhaser, only works with parent-child duos and does not compare
multiple children in a family. Handles only children outside nuclear families.'''
problem, params = request.problem, request.params
h = problem.haplotype
family_members = problem.families_union(min_children=0)
for parent_type in constants.ALLELES:
for child, parent in pt.selected_duos(problem, params, parent_type):
if not util.is_member(family_members, [child]):
ibd.phase_by_ibd(
request,
ip.ibd_segments_in_duo(
h,
parent,
child,
parent_type,
parent_het_fill_threshold=params.het_fill_threshold,
debug=params.debug), 'max')
return False
def __handle_all_duos(self, request):
'''Similar to __FamilyParentChildPhaser, only works with parent-child duos and does not compare
multiple children in a family. Handles all duos; processes children in pre-ordering (top-to-bottom
in the pedigree).'''
problem, params = request.problem, request.params
# Build all duos
duos = np.empty((0, 3), dtype=int)
for parent_type in constants.ALLELES:
d = problem.duos(parent_type)
duos = np.concatenate((duos, np.concatenate((d, np.tile(parent_type, (d.shape[0], 1))), axis=1)))
# Pre-order nodes
duos = duos[np.argsort([problem.pedigree.depth[x] for x in duos[:, 0]]), :]
h = problem.haplotype
for child, parent, parent_type in duos:
ibd.phase_by_ibd(problem,
ip.ibd_segments_in_duo(h, parent, child, parent_type,
parent_het_fill_threshold=params.het_fill_threshold,
debug=params.debug),
'max', debug=params.debug)
return False