def __phase_duo_child(self, problem, params, parent_type):
'''A helper method that phases a child based on a single parent of type parent_type.'''
# Find genotyped children whose parent is genotyped
duo = pt.selected_duos(problem, params, parent_type)
if not duo.size: return False
g, h = problem.data
gc, gp = g[:, duo[:, 0], :], g[:, duo[:, 1], :]
# Restrict view to snps that are homozygous in parent
hom = np.where(gt.is_homozygous(gp)[:, :])
parent_allele, gc_hom = gp[hom[0], hom[1], 0], gc[hom[0], hom[1], :]
#------------------------------------------------------------------------------------
# Case A: Parent = (a,a), child = (b,b) and a != b (incompatible) ==> error
#------------------------------------------------------------------------------------
j = np.where(
np.logical_and(
gt.is_homozygous(gc_hom)[:], gc_hom[:, 0] != parent_allele))[0]
# Flag errors in both children and parents
for i in xrange(2):
problem.genotype_error(hom[0][j], duo[hom[1][j], i],
'Homozygous parent allele not found in child')
#------------------------------------------------------------------------------------
# Case B: Parent = (a,a), child = (a,x) or (x,a), x in {0,1,2} (compatible) ==>
# set child parent hap to a and other hap to the other child genotype (x)
#------------------------------------------------------------------------------------
# Note: h[array,array,:] is not a reference into h like h[scalar,scalar,:]. Thus,
# when setting h, we must use h[original coordinates here] = ... . This occurs
# several times in the code of this file.
# Determine child haplotype corresponding to the hom parent
snps = gt.index_of(gc_hom, parent_allele)
parent_allele_at_snps = parent_allele[snps]
snp_index, child_index = hom[0][snps], duo[hom[1][snps], 0]
h[snp_index, child_index, parent_type] = parent_allele_at_snps
# Determine child haplotype corresponding to the other parent
gc_rel = g[snp_index, child_index, :]
other = np.where(
gc_rel != np.transpose(np.tile(parent_allele_at_snps, (2, 1))))
h[snp_index[other[0]], child_index[other[0]],
1 - parent_type] = gc_rel[other]
#------------------------------------------------------------------------------------
# Case C: Parent = (a,a), child = (0,x) or (x,0) (potentially compatible) ==>
# impute child to a and set child hap to a
#------------------------------------------------------------------------------------
for allele, snps in dict(zip(ALLELES,
gt.index_first_missing(gc_hom))).iteritems():
parent_value = parent_allele[snps]
snp_original = hom[0][snps]
gc[snp_original, hom[1][snps], allele] = parent_value
# if self.debug:
# print 'Imputing child', (snp_original, hom[1][snps], allele, parent_value)
# problem.info.imputed_genotype.append((snp_original, hom[1][snps], allele, parent_value))
h[snp_original, duo[hom[1][snps], 0], parent_type] = parent_value
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 __phase_duo_child(self, problem, params, parent_type):
'''A helper method that phases a child based on a single parent of type parent_type.'''
# Find genotyped children whose parent is genotyped
duo = pt.selected_duos(problem, params, parent_type)
if not duo.size: return False
g, h = problem.data
gc, gp = g[:, duo[:, 0], :], g[:, duo[:, 1], :]
# Restrict view to snps that are homozygous in parent
hom = np.where(gt.is_homozygous(gp)[:, :])
parent_allele, gc_hom = gp[hom[0], hom[1], 0], gc[hom[0], hom[1], :]
#------------------------------------------------------------------------------------
# Case A: Parent = (a,a), child = (b,b) and a != b (incompatible) ==> error
#------------------------------------------------------------------------------------
j = np.where(np.logical_and(gt.is_homozygous(gc_hom)[:], gc_hom[:, 0] != parent_allele))[0]
# Flag errors in both children and parents
for i in xrange(2): problem.genotype_error(hom[0][j], duo[hom[1][j], i], 'Homozygous parent allele not found in child')
#------------------------------------------------------------------------------------
# Case B: Parent = (a,a), child = (a,x) or (x,a), x in {0,1,2} (compatible) ==>
# set child parent hap to a and other hap to the other child genotype (x)
#------------------------------------------------------------------------------------
# Note: h[array,array,:] is not a reference into h like h[scalar,scalar,:]. Thus,
# when setting h, we must use h[original coordinates here] = ... . This occurs
# several times in the code of this file.
# Determine child haplotype corresponding to the hom parent
snps = gt.index_of(gc_hom, parent_allele)
parent_allele_at_snps = parent_allele[snps]
snp_index, child_index = hom[0][snps], duo[hom[1][snps], 0]
h[snp_index, child_index, parent_type] = parent_allele_at_snps
# Determine child haplotype corresponding to the other parent
gc_rel = g[snp_index, child_index, :]
other = np.where(gc_rel != np.transpose(np.tile(parent_allele_at_snps, (2, 1))))
h[snp_index[other[0]], child_index[other[0]], 1 - parent_type] = gc_rel[other]
#------------------------------------------------------------------------------------
# Case C: Parent = (a,a), child = (0,x) or (x,0) (potentially compatible) ==>
# impute child to a and set child hap to a
#------------------------------------------------------------------------------------
for allele, snps in dict(zip(ALLELES, gt.index_first_missing(gc_hom))).iteritems():
parent_value = parent_allele[snps]
snp_original = hom[0][snps]
gc[snp_original, hom[1][snps], allele] = parent_value
# if self.debug:
# print 'Imputing child', (snp_original, hom[1][snps], allele, parent_value)
# problem.info.imputed_genotype.append((snp_original, hom[1][snps], allele, parent_value))
h[snp_original, duo[hom[1][snps], 0], parent_type] = parent_value
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 __impute_duo_parent(problem, params, parent_type):
'''Child with two determined haps (a,b) and parent has (a,MISSING) or (MISSING,a) ==>
impute parent to (a,b). A helper method to process a single parent_type'''
duo = pt.selected_duos(problem, params, parent_type)
if not duo.size: return False
g, h = problem.data
gp, hc = g[:, duo[:, 1], :], h[:, duo[:, 0], :]
# Restrict view to SNPs with full child haplotype
child = np.where((hc[:, :, PATERNAL] != MISSING) & (hc[:, :, MATERNAL] != MISSING))
gp_rel, hc = gp[child[0], child[1], :], hc[child[0], child[1], :]
# Impute parent's first missing allele to be the corresponding child hap
for allele, snps in dict(zip(ALLELES, gt.index_first_missing(gp_rel))).iteritems():
hc_value = hc[snps, :, parent_type]
# if self.debug:
# print 'Imputing parent', (full[0][snps], duo[full[1][snps],1], allele)
# problem.info.imputed_genotype.append((full[0][snps], duo[full[1][snps],1], allele, hc_value))
g[child[0][snps], duo[child[1][snps], 1], allele] = hc_value
return False
def __impute_duo_parent(problem, params, parent_type):
'''Child with two determined haps (a,b) and parent has (a,MISSING) or (MISSING,a) ==>
impute parent to (a,b). A helper method to process a single parent_type'''
duo = pt.selected_duos(problem, params, parent_type)
if not duo.size: return False
g, h = problem.data
gp, hc = g[:, duo[:, 1], :], h[:, duo[:, 0], :]
# Restrict view to SNPs with full child haplotype
child = np.where((hc[:, :, PATERNAL] != MISSING)
& (hc[:, :, MATERNAL] != MISSING))
gp_rel, hc = gp[child[0], child[1], :], hc[child[0], child[1], :]
# Impute parent's first missing allele to be the corresponding child hap
for allele, snps in dict(zip(ALLELES,
gt.index_first_missing(gp_rel))).iteritems():
hc_value = hc[snps, :, parent_type]
# if self.debug:
# print 'Imputing parent', (full[0][snps], duo[full[1][snps],1], allele)
# problem.info.imputed_genotype.append((full[0][snps], duo[full[1][snps],1], allele, hc_value))
g[child[0][snps], duo[child[1][snps], 1], allele] = hc_value
return False
