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 __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 test_family_12(self):
'''Test comparing sibs with non-genotyped parents (stage 4).'''
problem = io.read_npz(itu.FAMILY12_STAGE2)
itu.assert_size_equals(problem.genotype, 3218, 7)
itu.assert_problem_stats(problem, 45052, 42162, 237)
assert_equal(len(list(problem.families(genotyped=False))), 1, 'Incorrect number of families')
phaser = family_sib_comparison_phaser()
phaser.run(problem, PhaseParam(single_member=1))
itu.assert_problem_stats(problem, 45052, 42162, 237)
def test_family_963(self):
'''Test comparing sibs with non-genotyped parents (stage 4). This was a problematic family.'''
problem = io.read_npz(itu.FAMILY963_STAGE4)
itu.assert_size_equals(problem.genotype, 3218, 3)
itu.assert_problem_stats(problem, 19308, 19286, 23)
assert_equal(len(list(problem.families(genotyped=False))), 1, 'Incorrect number of families')
phaser = family_sib_comparison_phaser()
phaser.run(problem)
itu.assert_problem_stats(problem, 19308, 19286, 23)
def test_family_12(self):
'''Test comparing sibs with non-genotyped parents (stage 4).'''
problem = io.read_npz(itu.FAMILY12_STAGE2)
itu.assert_size_equals(problem.genotype, 3218, 7)
itu.assert_problem_stats(problem, 45052, 42162, 237)
assert_equal(len(list(problem.families(genotyped=False))), 1,
'Incorrect number of families')
phaser = family_sib_comparison_phaser()
phaser.run(problem, PhaseParam(single_member=1))
itu.assert_problem_stats(problem, 45052, 42162, 237)
def test_family_963(self):
'''Test comparing sibs with non-genotyped parents (stage 4). This was a problematic family.'''
problem = io.read_npz(itu.FAMILY963_STAGE4)
itu.assert_size_equals(problem.genotype, 3218, 3)
itu.assert_problem_stats(problem, 19308, 19286, 23)
assert_equal(len(list(problem.families(genotyped=False))), 1,
'Incorrect number of families')
phaser = family_sib_comparison_phaser()
phaser.run(problem)
itu.assert_problem_stats(problem, 19308, 19286, 23)
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 test_family_2003_need_poo_alignment(self):
'''Test comparing sibs with non-genotyped parents (stage 4). This case highlights
the need to align POO-phases, i.e., swap founder haps to correctly patch families at individual
ID 28412 (our original index 386; in this problem, index 10).'''
problem = io.read_npz(itu.FAMILY2003_STAGE3)
itu.assert_size_equals(problem.genotype, 3218, 9)
itu.assert_problem_stats(problem, 57924, 43339, 85)
assert_equal(len(list(problem.families(genotyped=False))), 1, 'Incorrect number of families')
#f = problem.families(genotyped=False)[0]
#print f.member_list
#print problem.pedigree.sample_id
phaser = family_sib_comparison_phaser()
phaser.run(problem)
itu.assert_problem_stats(problem, 57924, 57515, 85)
def test_family_2003_need_poo_alignment(self):
'''Test comparing sibs with non-genotyped parents (stage 4). This case highlights
the need to align POO-phases, i.e., swap founder haps to correctly patch families at individual
ID 28412 (our original index 386; in this problem, index 10).'''
problem = io.read_npz(itu.FAMILY2003_STAGE3)
itu.assert_size_equals(problem.genotype, 3218, 9)
itu.assert_problem_stats(problem, 57924, 43339, 85)
assert_equal(len(list(problem.families(genotyped=False))), 1,
'Incorrect number of families')
#f = problem.families(genotyped=False)[0]
#print f.member_list
#print problem.pedigree.sample_id
phaser = family_sib_comparison_phaser()
phaser.run(problem)
itu.assert_problem_stats(problem, 57924, 57515, 85)