def pipeline_validation_experiment(location_file, true_type, true_location, pedigree, debug=False, remove_partial_calls=False):
'''Load (the ''true'') genotypes from an external source. Load a list of locations from ''location_file''. Impute them and compare
with the true genotypes.'''
g = extract_genotypes(location_file)
t = ImputationSet(pedigree, g)
if true_type == 'iplex': true_genotype = im.imputation.reader.iplex_to_genotype(true_location, t) # os.environ['OBER'] + '/data/impute/rare/to_livne_20121205', t)
else: raise ValueError('Unsupported true genotype format ''%s''' % (true_type,))
problem = Problem(pedigree, true_genotype)
p, t = impute_problem(problem, debug=debug, remove_partial_calls=remove_partial_calls)
return p, t
#!/usr/bin/env python ''' ============================================================ Hutt Kids - compute chr 22 phasing stats. Created on July 15, 2013 @author: Oren Livne <*****@*****.**> ============================================================ ''' import impute as im, os, numpy as np from impute.imputation.ImputationSet import ImputationSet path = os.environ['OBER_OUT'] + '/kids' chrom = 22 prefix = path + '/cytosnp/chr%d/cytosnp.imputed' % (chrom,) # Load phasing result problem = im.io.read_npz(prefix + '.phased.npz') t = ImputationSet.from_problem(problem) c = im.v.iv.stats_computer(t, problem.g) s = c.stats()
def test_read_snps_to_impute(self):
'''Test loading SNPs to be imputed from an NPZ file generated with cgi2plink
(by way of io_genotype.write()).'''
a = ImputationSet.load(im.itu.IMPUTE_RARE)
g = a.genotype
assert_size_equals(g, 146, 98)
