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 setUp(self):
'''Load test data and expected results.'''
unittest.TestCase.setUp(self)
# Test phaser, doesn't matter which here
self.phaser = new_phaser_chain([trivial_phaser()])
# Generate a non-trivial Problem
self.problem = itu.Templates.problem_family(itu.FAMILY13, haplotype=True)
def family_sib_comparison_phaser(next_filter=None, debug=False, print_times=False):
chain = [
FamilyPhaser(family_handle=__handle_sib_comparison, name='* Sibs', genotyped_families=False),
phased_samples_phaser # In selected samples mode, reset all non-selected haplotypes back to the original values
]
return new_phaser_chain(chain, name='Family Sib', next_filter=next_filter,
debug=debug, print_times=print_times)
def trivial_phaser(next_filter=None, debug=False, print_times=False):
return new_phaser_chain([
Filter(name='* Hom SNPs', handle=__handle_hom_entries),
Filter(name='* Hom Parent', handle=__handle_hom_parent),
Filter(name='* Impute Parent', handle=__handle_impute_parent),
phased_samples_phaser # In selected samples mode, reset all non-selected haplotypes back to the original values
], name='Trivial Cases', debug=debug, print_times=print_times)
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.problem = io.read_plink(pedigree=itu.HUTT_PED, prefix=itu.GENOTYPE_SAMPLE, haplotype=None)
self.phaser = new_phaser_chain([trivial_phaser()])
def prepare_phaser(next_filter=None, debug=False, print_times=False):
return new_phaser_chain(
[estimate_frequencies_phaser, phased_samples_phaser],
name="Pre-Processing",
debug=debug,
print_times=print_times,
)
def family_child_comparison_phaser(next_filter=None, debug=False, print_times=False):
chain = [
Filter(name='* Child Comparison', handle=__handle_child_comparison),
phased_samples_phaser # In selected samples mode, reset all non-selected haplotypes back to the original values
]
return new_phaser_chain(chain, name='Family Children', next_filter=next_filter,
debug=debug, print_times=print_times)
def save_stats_processor(next_filter=None, debug=False, print_times=False):
return new_phaser_chain([
estimate_frequencies_phaser,
Filter(name='* Save stats', handle=__handle_save_stats)
],
name='Save Stats',
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 prepare_phaser(next_filter=None, debug=False, print_times=False):
return new_phaser_chain([
estimate_frequencies_phaser,
phased_samples_phaser,
],
name='Pre-Processing',
debug=debug,
print_times=print_times)
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.problem = io.read_plink(pedigree=itu.HUTT_PED,
prefix=itu.GENOTYPE_SAMPLE,
haplotype=None)
self.phaser = new_phaser_chain([trivial_phaser()])
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 family_phaser(next_filter=None, debug=False, single_family=False, print_times=False):
chain = [
Filter(name='* Outer Duos', handle=__handle_outer_duos, debug=debug),
# Phaser(name='* All Duos', handle=__handle_all_duos, debug=debug),
FamilyPhaser(family_handle=__handle_parent_child, genotyped_families=True, min_children=0,
name='* Phased Parent->Child'),
phased_samples_phaser # In selected samples mode, reset all non-selected haplotypes back to the original values
]
return new_phaser_chain(chain, name='Family Parent-Child', next_filter=next_filter,
debug=debug, print_times=print_times)
def trivial_phaser(next_filter=None, debug=False, print_times=False):
return new_phaser_chain(
[
Filter(name='* Hom SNPs', handle=__handle_hom_entries),
Filter(name='* Hom Parent', handle=__handle_hom_parent),
Filter(name='* Impute Parent', handle=__handle_impute_parent),
phased_samples_phaser # In selected samples mode, reset all non-selected haplotypes back to the original values
],
name='Trivial Cases',
debug=debug,
print_times=print_times)
def distant_phaser(next_filter=None, debug=False, print_times=False,
max_samples=np.inf, single_sample=None):
chain = [
__ParentDistantPhaser(name='* Distant IBD',
max_samples=max_samples,
single_sample=single_sample,
debug=debug),
phased_samples_phaser # In selected samples mode, reset all non-selected haplotypes back to the original values
]
return new_phaser_chain(chain, name='Distant IBD', next_filter=next_filter,
debug=debug, print_times=print_times)
def family_child_comparison_phaser(next_filter=None,
debug=False,
print_times=False):
chain = [
Filter(name='* Child Comparison', handle=__handle_child_comparison),
phased_samples_phaser # In selected samples mode, reset all non-selected haplotypes back to the original values
]
return new_phaser_chain(chain,
name='Family Children',
next_filter=next_filter,
debug=debug,
print_times=print_times)
def family_sib_comparison_phaser(next_filter=None,
debug=False,
print_times=False):
chain = [
FamilyPhaser(family_handle=__handle_sib_comparison,
name='* Sibs',
genotyped_families=False),
phased_samples_phaser # In selected samples mode, reset all non-selected haplotypes back to the original values
]
return new_phaser_chain(chain,
name='Family Sib',
next_filter=next_filter,
debug=debug,
print_times=print_times)
def distant_phaser(next_filter=None,
debug=False,
print_times=False,
max_samples=np.inf,
single_sample=None):
chain = [
__ParentDistantPhaser(name='* Distant IBD',
max_samples=max_samples,
single_sample=single_sample,
debug=debug),
phased_samples_phaser # In selected samples mode, reset all non-selected haplotypes back to the original values
]
return new_phaser_chain(chain,
name='Distant IBD',
next_filter=next_filter,
debug=debug,
print_times=print_times)
def family_phaser(next_filter=None,
debug=False,
single_family=False,
print_times=False):
chain = [
Filter(name='* Outer Duos', handle=__handle_outer_duos, debug=debug),
# Phaser(name='* All Duos', handle=__handle_all_duos, debug=debug),
FamilyPhaser(family_handle=__handle_parent_child,
genotyped_families=True,
min_children=0,
name='* Phased Parent->Child'),
phased_samples_phaser # In selected samples mode, reset all non-selected haplotypes back to the original values
]
return new_phaser_chain(chain,
name='Family Parent-Child',
next_filter=next_filter,
debug=debug,
print_times=print_times)
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()])
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_phasing_pipeline(options):
'''Bulid and return the entire phasing processing chain by options - factory method.'''
chain = __build_phaser(options) + __build_post_chain(options)
return new_phaser_chain(chain,
debug=options.debug,
print_times=options.print_times)
def save_stats_processor(next_filter=None, debug=False, print_times=False):
return new_phaser_chain([
estimate_frequencies_phaser,
Filter(name='* Save stats', handle=__handle_save_stats)
], name='Save Stats', debug=debug, print_times=print_times)
def build_phasing_pipeline(options):
'''Bulid and return the entire phasing processing chain by options - factory method.'''
chain = __build_phaser(options) + __build_post_chain(options)
return new_phaser_chain(chain, debug=options.debug, print_times=options.print_times)
def prepare_and_trivial_phaser(debug=False, print_times=False):
return new_phaser_chain([
prepare_phaser(),
trivial_phaser()
], debug=debug, print_times=print_times)