def write(self, genotype, out, **kwargs):
'''Write genotype data to the stream out in IMPUTE2 haplotype format. If snps is specified,
only those snp indices are written, otherwise all snps are written.'''
# Read optional arguments; truncate data accordingly
snps = kwargs.get('snps', genotype.snp_range)
samples = kwargs.get('samples', np.arange(genotype.num_samples))
flip_alleles = kwargs.get('flip_alleles',
np.zeros(len(snps), dtype=bool))
# Zero out partially-called genotypes (an IMPUTE2 requirement)
data = genotype.data[snps][:, samples, :].copy()
recode.clear_partial_calls(data)
# Convert SNP data to string
snp_metadata = genotype.snp[
snps] # [np.array(['chrom', 'name', 'dist_cm', 'base_pair'])]
snp_as_string = np.array([str(y) for x in snp_metadata
for y in x]).reshape((len(snps), 4))
# Recode alleles + missing data
recoding = {MISSING: '?', 1: '0', 2: '1'}
r = np.vectorize(recoding.__getitem__)
data_str = r(data)
# Flip alleles
recoding_flipped = {MISSING: '?', 1: '1', 2: '0'}
r = np.vectorize(recoding_flipped.__getitem__)
data_str[flip_alleles] = r(data[flip_alleles])
for i in xrange(len(snps)):
np.savetxt(out, snp_as_string[i], fmt='%s', newline=' ')
np.savetxt(out, data_str[i, :, :], fmt='%s', newline=' ')
out.write('\n')
def write(self, genotype, out, **kwargs):
"""Write genotype data to the stream out in IMPUTE2 haplotype format. If snps is specified,
only those snp indices are written, otherwise all snps are written."""
# Read optional arguments; truncate data accordingly
snps = kwargs.get("snps", genotype.snp_range)
samples = kwargs.get("samples", np.arange(genotype.num_samples))
flip_alleles = kwargs.get("flip_alleles", np.zeros(len(snps), dtype=bool))
# Zero out partially-called genotypes (an IMPUTE2 requirement)
data = genotype.data[snps][:, samples, :].copy()
recode.clear_partial_calls(data)
# Convert SNP data to string
snp_metadata = genotype.snp[snps] # [np.array(['chrom', 'name', 'dist_cm', 'base_pair'])]
snp_as_string = np.array([str(y) for x in snp_metadata for y in x]).reshape((len(snps), 4))
# Recode alleles + missing data
recoding = {MISSING: "?", 1: "0", 2: "1"}
r = np.vectorize(recoding.__getitem__)
data_str = r(data)
# Flip alleles
recoding_flipped = {MISSING: "?", 1: "1", 2: "0"}
r = np.vectorize(recoding_flipped.__getitem__)
data_str[flip_alleles] = r(data[flip_alleles])
for i in xrange(len(snps)):
np.savetxt(out, snp_as_string[i], fmt="%s", newline=" ")
np.savetxt(out, data_str[i, :, :], fmt="%s", newline=" ")
out.write("\n")
def __handle_impute_from_fully_called(self, request):
'''A request handler that imputes missing genotypes in g from fully-called haplotypes h. Clear
partially-called genotypes.'''
(g, h) = request.problem.data
num_imputed = impute_from_fully_called(g, h)
if request.params.debug: print 'Imputed %d genotypes' % (num_imputed,)
# Zero-out partial haplotypes. Note: PLINK requires full genotypes, so expect failure
# if this option is turned off. Therefore it is always on, and we only impute from FULLY called
# haps above.
recode.clear_partial_calls(g)
return False
def __handle_impute_from_fully_called(self, request):
'''A request handler that imputes missing genotypes in g from fully-called haplotypes h. Clear
partially-called genotypes.'''
(g, h) = request.problem.data
num_imputed = impute_from_fully_called(g, h)
if request.params.debug: print 'Imputed %d genotypes' % (num_imputed, )
# Zero-out partial haplotypes. Note: PLINK requires full genotypes, so expect failure
# if this option is turned off. Therefore it is always on, and we only impute from FULLY called
# haps above.
recode.clear_partial_calls(g)
return False