def __init__(self, g_orig, haplotype, num_errors):
'''Initialize phasing statistics object for the original genotype g/and haplotype set problem.haplotype.'''
h = haplotype.data
r_orig = recode.recode_single_genotype(g_orig)
r = recode.recode_single_genotype(h)
# Sizes
self.time = 0
self.num_snps = haplotype.num_snps
self.num_samples = haplotype.num_samples
self.num_genotypes = haplotype.num_data / 2
self.num_haplotypes = haplotype.num_data
# Arrays
self.fill = np.array([haplotype.fill_fraction(sample=x) for x in xrange(haplotype.num_samples)])
# Fields
# A Field factory method
field = lambda index: StatsField(self, h, index)
self.called_orig = field(recode.where_called(r_orig))
self.imputed = field(recode.where_full_imputed(r, r_orig))
self.imputed_partial = field(recode.where_partial_imputed(r, r_orig))
self.errors = field(recode.where_error(r, r_orig))
self.errors_partial = field(recode.where_partial_error(r, r_orig))
self.called = field(recode.where_called(r))
self.partial_called = field(recode.where_partial_called(r))
self.still_missing = field(recode.where_still_missing(r, r_orig))
# Scalars
self.num_filled_haplotypes = haplotype.num_filled
self.num_errors = num_errors # Redundant
def __init__(self, g_orig, haplotype, num_errors):
'''Initialize phasing statistics object for the original genotype g/and haplotype set problem.haplotype.'''
h = haplotype.data
r_orig = recode.recode_single_genotype(g_orig)
r = recode.recode_single_genotype(h)
# Sizes
self.time = 0
self.num_snps = haplotype.num_snps
self.num_samples = haplotype.num_samples
self.num_genotypes = haplotype.num_data / 2
self.num_haplotypes = haplotype.num_data
# Arrays
self.fill = np.array([
haplotype.fill_fraction(sample=x)
for x in xrange(haplotype.num_samples)
])
# Fields
# A Field factory method
field = lambda index: StatsField(self, h, index)
self.called_orig = field(recode.where_called(r_orig))
self.imputed = field(recode.where_full_imputed(r, r_orig))
self.imputed_partial = field(recode.where_partial_imputed(r, r_orig))
self.errors = field(recode.where_error(r, r_orig))
self.errors_partial = field(recode.where_partial_error(r, r_orig))
self.called = field(recode.where_called(r))
self.partial_called = field(recode.where_partial_called(r))
self.still_missing = field(recode.where_still_missing(r, r_orig))
# Scalars
self.num_filled_haplotypes = haplotype.num_filled
self.num_errors = num_errors # Redundant
def impute_from_fully_called(g, h):
'''Impute missing genotypes in g from fully-called haplotypes h. The imputation is typically done on the
genotypes after phasing, which may contain zeroed-out entries found to be Mendelian errors, and thus
will benefit from imputation here. Partially-filled genotypes are also overridden by haps, if the
latter are fully called. Returns the number of imputed genotypes'''
imputed = recode.where_full_imputed(recode.recode_single_genotype(h), recode.recode_single_genotype(g))
g[imputed[SNP], imputed[SAMPLE], :] = h[imputed[SNP], imputed[SAMPLE], :]
return len(imputed[0])
def impute_from_fully_called(g, h):
'''Impute missing genotypes in g from fully-called haplotypes h. The imputation is typically done on the
genotypes after phasing, which may contain zeroed-out entries found to be Mendelian errors, and thus
will benefit from imputation here. Partially-filled genotypes are also overridden by haps, if the
latter are fully called. Returns the number of imputed genotypes'''
imputed = recode.where_full_imputed(recode.recode_single_genotype(h),
recode.recode_single_genotype(g))
g[imputed[SNP], imputed[SAMPLE], :] = h[imputed[SNP], imputed[SAMPLE], :]
return len(imputed[0])