def __init__(self, family_handle, next_filter=None, name=None,
genotyped_families=True, min_children=0):
'''Initialize a filter that uses the filter processor to process SNP+trio combinations.
Use single_family in debugging to process only the first encountered family.'''
Filter.__init__(self, name=name, next_filter=next_filter)
self.family_handle = family_handle
self.genotyped_families = genotyped_families
self.min_children = min_children
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 __init__(self,
next_filter=None,
name=None,
single_sample=None,
max_samples=np.inf,
debug=False):
Filter.__init__(self, name=name, next_filter=next_filter)
# Debugging options
self.single_sample = single_sample
self.debug = debug
self.max_samples = max_samples
def __init__(self,
family_handle,
next_filter=None,
name=None,
genotyped_families=True,
min_children=0):
'''Initialize a filter that uses the filter processor to process SNP+trio combinations.
Use single_family in debugging to process only the first encountered family.'''
Filter.__init__(self, name=name, next_filter=next_filter)
self.family_handle = family_handle
self.genotyped_families = genotyped_families
self.min_children = min_children
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 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_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)
in selected_samples are to be phased, while the remaining are already phased.'''
# Load problem fields
if request.params.selected_mode:
phased = np.array(
list(
set(range(request.problem.num_samples)) -
set(request.params.selected_samples)))
g, h = request.problem.data
h[:, phased, :] = g[:, phased, :]
return False
####################################################################################
'''Main pre-processing chain - a facade.'''
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)
estimate_frequencies_phaser = Filter(
name='* Genotype Freq', handle=__handle_estimate_genotype_frequencies)
phased_samples_phaser = Filter(name='* Phased Samples',
handle=__handle_phased_samples)
def __init__(self, delegate, next_filter=None):
'''Initialize a decorator of the delegate Filter. fmt specifies the printout format string that
accepts one string argument for the filter's name.'''
Filter.__init__(self, next_filter=next_filter, name=delegate.name)
self.delegate = delegate
def fill_missing_processor(next_filter=None, debug=False, print_times=False):
return Filter(name='* Fill Missing',
handle=__handle_fill_missing_genotypes)
def impute_processor(next_filter=None, debug=False, print_times=False):
return Filter(name='* Impute from Fully-Called',
handle=__handle_impute_from_fully_called)
def __init__(self, increment, next_filter=None):
'''Initialize a filter.'''
Filter.__init__(self, next_filter)
self.increment = increment
def __init__(self, next_filter=None, name=None, single_sample=None, max_samples=np.inf, debug=False):
Filter.__init__(self, name=name, next_filter=next_filter)
# Debugging options
self.single_sample = single_sample
self.debug = debug
self.max_samples = max_samples
def __init__(self, delegate, next_filter=None):
'''Initialize a decorator of the delegate Filter. fmt specifies the printout format string that
accepts one string argument for the filter's name.'''
Filter.__init__(self, next_filter=next_filter, name=delegate.name)
self.delegate = delegate
def __init__(self, increment, next_filter=None):
'''Initialize a filter.'''
Filter.__init__(self, next_filter)
self.increment = increment
