def phaser_stages13(debug=False, print_times=False):
return new_phaser_chain([
prepare_phaser(),
trivial_phaser(),
family_phaser(),
family_child_comparison_phaser(),
], debug=debug, print_times=print_times)
def nuclear_family_phaser(debug=False, print_times=False):
return new_phaser_chain([
prepare_phaser(),
trivial_phaser(),
family_phaser(),
family_child_comparison_phaser(),
family_sib_comparison_phaser(),
], debug=debug, print_times=print_times)
def phaser_stages13(debug=False, print_times=False):
return new_phaser_chain([
prepare_phaser(),
trivial_phaser(),
family_phaser(),
family_child_comparison_phaser(),
],
debug=debug,
print_times=print_times)
def __build_phaser(options):
'''Bulid and return the phasing processing chain by options - factory method.'''
if options.stage == 0:
# 07-DEC-12: disabling stage 4 (family_sib_comparison_phaser) since it degrades phasing & imputation
chain = [
prepare_phaser(),
trivial_phaser(),
family_phaser(),
family_child_comparison_phaser(),
phase_distant.family_sib_comparison_phaser(),
phase_distant.distant_phaser()
]
elif options.stage == 1: chain = [prepare_phaser(), trivial_phaser()]
elif options.stage == 2: chain = [family_phaser()]
elif options.stage == 3: chain = [family_child_comparison_phaser()]
elif options.stage == 4: chain = [phase_distant.family_sib_comparison_phaser()]
elif options.stage == 5: chain = [phase_distant.distant_phaser()]
return chain
def nuclear_family_phaser(debug=False, print_times=False):
return new_phaser_chain([
prepare_phaser(),
trivial_phaser(),
family_phaser(),
family_child_comparison_phaser(),
family_sib_comparison_phaser(),
],
debug=debug,
print_times=print_times)
def setUp(self):
'''Load test data and expected results.'''
unittest.TestCase.setUp(self)
# Load test data ready from previous phasing stagees
self.problem = io.read_npz(itu.FAMILY_TOO_ZEROED_STAGE1)
self.family = self.problem.families()[0]
self.phaser = phase_core.PhaseDecorator(FilterChain([trivial_phaser(),
family_phaser(),
family_child_comparison_phaser()]))
self.comparator = ic.ChildComparator(Struct(problem=self.problem, params=PhaseParam()), self.family)
def __build_phaser(options):
'''Bulid and return the phasing processing chain by options - factory method.'''
if options.stage == 0:
# 07-DEC-12: disabling stage 4 (family_sib_comparison_phaser) since it degrades phasing & imputation
chain = [
prepare_phaser(),
trivial_phaser(),
family_phaser(),
family_child_comparison_phaser(),
phase_distant.family_sib_comparison_phaser(),
phase_distant.distant_phaser()
]
elif options.stage == 1:
chain = [prepare_phaser(), trivial_phaser()]
elif options.stage == 2:
chain = [family_phaser()]
elif options.stage == 3:
chain = [family_child_comparison_phaser()]
elif options.stage == 4:
chain = [phase_distant.family_sib_comparison_phaser()]
elif options.stage == 5:
chain = [phase_distant.distant_phaser()]
return chain
def setUp(self):
'''Load test data and expected results.'''
unittest.TestCase.setUp(self)
# Load test data ready from previous phasing stagees
self.problem = io.read_npz(itu.FAMILY13_STAGE2)
self.family = self.problem.families()[0]
self.phaser = phase_core.PhaseDecorator(
FilterChain([
trivial_phaser(),
family_phaser(),
family_child_comparison_phaser()
]))
self.comparator = ic.ChildComparator(
Struct(problem=self.problem, params=PhaseParam()), self.family)
def test_outer_duo(self):
'''Test applying child comparison to a nuclear family with many genotyped kids but only
one genotyped parent. Seems to be fine for now: too many errors are flagged, but we are not
going to split hair.'''
p = self.problem
# h = p.haplotype
# (f, m) = (self.family.father, self.family.mother)
snp = p.info.snp_by_name('rs5746679')
assert_equal(snp, [3], 'Wrong SNP index')
itu.assert_size_equals(p.genotype, 3218, 7)
itu.assert_problem_stats(p, 45052, 40086, 4)
# print 'genotypes'
# print p.genotype.data[snp, :, :]
# print 'haplotypes'
# print p.haplotype.data[snp, :, :]
phaser = family_phaser()
phaser.run(p)
itu.assert_problem_stats(p, 45052, 45023, 25)
def setUp(self):
'''Load test data and expected results.'''
unittest.TestCase.setUp(self)
# The way to load a pedigree in conjunction with a genotype set is to recode
# its sample IDs to consecutive for easier access by phasers.
self.phaser = new_phaser_chain([trivial_phaser(), family_phaser(), family_child_comparison_phaser()])
