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()