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 __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 prepare_and_trivial_phaser(debug=False, print_times=False):
return new_phaser_chain(
[prepare_phaser(), trivial_phaser()],
debug=debug,
print_times=print_times)
def __build_pre_phaser(options):
# if options.stage != 0:
# return []
return [prepare_phaser()]
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 = prepare_phaser()
