def phase_parent_by_template(self, info):
'''Impute the parent haplotype. A random parent random phase is selected and switched at
each recombination location in the template child.'''
bp = self.problem.info.snp['base_pair']
num_snps = self.problem.num_snps
parent = info.parent
child = info.template_child
parent_type = info.parent_type
if self.params.debug:
print 'phase_parent_by_template(parent=%d, template=%d, parent_type=%d)' % (parent, child, parent_type)
# h = problem.haplotype.data
# Infer the parent's haplotypes from the template child's recombinations r
r = info.recombination_snp
edge = [y for (x, y) in r if x == child]
# r = np.concatenate(([-1], edge, [problem.num_snps-1]))
phase = PATERNAL # Random phase set at the starting of the chromosome
segments = segment.edges_to_segments(self.problem.snp_range, edge, phase,
self.problem.num_snps, cover=True)
segment_set = SegmentSet((Segment((x[0], x[1]), ((parent, x[2]), (child, parent_type)),
(bp[x[0]], im.segment.stop_bp(bp, x[1], num_snps)))
for x in segments))
# Only a single sweep suffices here, since only two samples are involved. If a homogeneous
# entry is discovered and used to propagate phases in the second of the two IBD sets in
# a SNP range, there's no need to fix the first one since the data is already fully filled.
ibd.phase_by_ibd(self.request, [segment_set], 'max', num_sweeps=1)
def ibs_segments(self):
'''Convert recombinations r to IBD segments. A generator.'''
if not self.snps_exist:
return
r = self.recombination_index
bp = self.problem.info.snp['base_pair']
# print r
# Calculate IBD segments between all children and parent
for child in self.children:
# print '-------------------- child %d ----------------------' % (child,)
edge = [y for (x, y) in r if x == child]
phase = PATERNAL # Random phase set at the starting of the chromosome
segments = segment.edges_to_segments(self.snps, edge, phase, self.num_snps, cover=True)
if self.debug:
print 'child', child, 'edge', edge, 'segments', segments
# Flip initial phase if parent is phased at hap snps by comparing its
# haplotypes with the child haplotypes on the longest IBD segment
i = np.argmax(np.diff(segments)[:, 0])
segment_phase = phase if np.mod(i, 2) == 0 else 1 - phase
actual_phase = self.__equal_parent_hap(child, segments[i, 0], segments[i, 1])
if segment_phase != actual_phase:
segments = segment.flip_phase(segments)
# Output segments in the standard IBD segment format
yield SegmentSet((Segment((x[0], x[1]), ((self.parent, x[2]), (child, self.parent_type)),
(bp[x[0]], im.segment.stop_bp(bp, x[1], self.num_snps)))
for x in segments))
def phase_parent_by_template(self, info):
'''Impute the parent haplotype. A random parent random phase is selected and switched at
each recombination location in the template child.'''
bp = self.problem.info.snp['base_pair']
num_snps = self.problem.num_snps
parent = info.parent
child = info.template_child
parent_type = info.parent_type
if self.params.debug:
print 'phase_parent_by_template(parent=%d, template=%d, parent_type=%d)' % (
parent, child, parent_type)
# h = problem.haplotype.data
# Infer the parent's haplotypes from the template child's recombinations r
r = info.recombination_snp
edge = [y for (x, y) in r if x == child]
# r = np.concatenate(([-1], edge, [problem.num_snps-1]))
phase = PATERNAL # Random phase set at the starting of the chromosome
segments = segment.edges_to_segments(self.problem.snp_range,
edge,
phase,
self.problem.num_snps,
cover=True)
segment_set = SegmentSet(
(Segment((x[0], x[1]), ((parent, x[2]), (child, parent_type)),
(bp[x[0]], im.segment.stop_bp(bp, x[1], num_snps)))
for x in segments))
# Only a single sweep suffices here, since only two samples are involved. If a homogeneous
# entry is discovered and used to propagate phases in the second of the two IBD sets in
# a SNP range, there's no need to fix the first one since the data is already fully filled.
ibd.phase_by_ibd(self.request, [segment_set], 'max', num_sweeps=1)
def ibs_segments(self):
'''Convert recombinations r to IBD segments. A generator.'''
if not self.snps_exist:
return
r = self.recombination_index
bp = self.problem.info.snp['base_pair']
# print r
# Calculate IBD segments between all children and parent
for child in self.children:
# print '-------------------- child %d ----------------------' % (child,)
edge = [y for (x, y) in r if x == child]
phase = PATERNAL # Random phase set at the starting of the chromosome
segments = segment.edges_to_segments(self.snps,
edge,
phase,
self.num_snps,
cover=True)
if self.debug:
print 'child', child, 'edge', edge, 'segments', segments
# Flip initial phase if parent is phased at hap snps by comparing its
# haplotypes with the child haplotypes on the longest IBD segment
i = np.argmax(np.diff(segments)[:, 0])
segment_phase = phase if np.mod(i, 2) == 0 else 1 - phase
actual_phase = self.__equal_parent_hap(child, segments[i, 0],
segments[i, 1])
if segment_phase != actual_phase:
segments = segment.flip_phase(segments)
# Output segments in the standard IBD segment format
yield SegmentSet((Segment(
(x[0], x[1]), ((self.parent, x[2]), (child, self.parent_type)),
(bp[x[0]], im.segment.stop_bp(bp, x[1], self.num_snps)))
for x in segments))
def ibs_segments(haplotype,
id1,
id2,
hap1_type,
hap2_type,
snps=None,
include_alt_phase=False,
error_filter='median',
error_filter_length=5,
length_bound=None,
min_segment_length=INDETERMINATE,
margin=0.0,
debug=False):
'''Return 1) Identical-by-State (IBS) segments separated by recombination events between two
sample haplotypes (id1, hap1_type) and (id2, hap2_type). The 2-D output array's ith row format is
(segment_start, segment_stop),
(id1, hap1), (id2, hap2),
(segment_start_bp, segment_stop_bp, segment_length_in_bp, num_errors_in_segment)
The SNP range is [segment_start, segment_stop) where start=inclusive and stop is exclusive.
2) List of het_snp indices at which there are likely genotype errors.
Options:
snps - list of SNPs to base the comparison on. For parent-child comparisons, these should
be heterozygous SNPs in the parent's genotype, distinguishing its haplotypes
and used to locate segments. For unphased-phased individuals, these should be the list of
homozygous SNPs at the unphased individual (those that have data).
If not specified, all SNPs are used.
length_bound - minimum segment length bound type:
None: no lower bound enforced
'base_pair': output segments of at least min_segment_length [base pair]
'snp': output segments of at least min_segment_length consecutive SNPs out of the snps list.
This is useful only if snps includes all SNPs (or is None)
*NOTE*: min_segment_length''s units are interpreted differently depending on length_bound.
margin = fraction of segment to discard near the endpoints (margin/2 is removed from each side).'''
if debug:
print 'Computing IBD segments between haplotypes (%d,%d), (%d,%d); filter %s length %d' % \
(id1, hap1_type, id2, hap2_type, error_filter, error_filter_length)
d = diff.all_diffs(haplotype.data,
id1,
id2,
hap1_type=hap1_type,
hap2_type=hap2_type)[0]
# Segment length, as defined by the input parameters
segment_length = lambda f: np.inf if not length_bound else (
f.length
if length_bound == 'base_pair' else f.num_snps) # @UnusedVariable
# Consider informative or the specified SNPs only
snps = snps if snps is not None else haplotype.snp_range
snps = np.intersect1d(snps, np.where(d != INDETERMINATE)[0])
d_snps = d[snps]
filtered_diff = filter_diff(d_snps, error_filter, error_filter_length)
error_snps = snps[np.nonzero(d_snps - filtered_diff)[0]]
# Detect edges as non-zero gradient points; output sufficiently long segments
bp = haplotype.snp['base_pair']
num_snps = haplotype.num_snps
if np.size(filtered_diff) == 0:
# No data to consider ==> no IBD intervals can be identified
segments = []
else:
deriv = ndimage.convolve(filtered_diff, [1, -1])
edge = np.where(deriv != 0)[0]
initial_phase = hap1_type if filtered_diff[0] == 0 else 1 - hap1_type
if debug:
print 'initial_phase', initial_phase # , 'edge', edge
# Convert recombination locations to segments of no recombination; filter short segments
segments = [
f for f in (
Segment(((x[0], x[1])),
set(((id1, x[2]), (id2, hap2_type))), (
bp[x[0]], segment.stop_bp(bp, x[1], num_snps)),
error_snps=segment.in_segment(error_snps, x))
for x in segment.edges_to_segments(
snps, edge, initial_phase, haplotype.num_snps, hap1_type))
if segment_length(f) >= min_segment_length
]
# Cut segment margins
if margin >= constants.SMALL_FLOAT:
segments = [
s for s in (s.middle_part(haplotype.nearest_snp, bp, margin)
for s in segments) if s
]
# Restrict errors to those inside segments
segment_set = SegmentSet(segments,
np.array(util.flattened_meshgrid(reduce(list.__add__, (s.error_snps.tolist() for s in segments)),
np.array([id1, id2])), dtype=int) \
if segments else gt.empty_errors_array())
if debug:
print 'ibs_segments()', segment_set
print 'errors', segment_set.errors
return segment_set
def ibs_segments(haplotype, id1, id2, hap1_type, hap2_type, snps=None, include_alt_phase=False,
error_filter='median', error_filter_length=5,
length_bound=None, min_segment_length=INDETERMINATE, margin=0.0, debug=False):
'''Return 1) Identical-by-State (IBS) segments separated by recombination events between two
sample haplotypes (id1, hap1_type) and (id2, hap2_type). The 2-D output array's ith row format is
(segment_start, segment_stop),
(id1, hap1), (id2, hap2),
(segment_start_bp, segment_stop_bp, segment_length_in_bp, num_errors_in_segment)
The SNP range is [segment_start, segment_stop) where start=inclusive and stop is exclusive.
2) List of het_snp indices at which there are likely genotype errors.
Options:
snps - list of SNPs to base the comparison on. For parent-child comparisons, these should
be heterozygous SNPs in the parent's genotype, distinguishing its haplotypes
and used to locate segments. For unphased-phased individuals, these should be the list of
homozygous SNPs at the unphased individual (those that have data).
If not specified, all SNPs are used.
length_bound - minimum segment length bound type:
None: no lower bound enforced
'base_pair': output segments of at least min_segment_length [base pair]
'snp': output segments of at least min_segment_length consecutive SNPs out of the snps list.
This is useful only if snps includes all SNPs (or is None)
*NOTE*: min_segment_length''s units are interpreted differently depending on length_bound.
margin = fraction of segment to discard near the endpoints (margin/2 is removed from each side).'''
if debug:
print 'Computing IBD segments between haplotypes (%d,%d), (%d,%d); filter %s length %d' % \
(id1, hap1_type, id2, hap2_type, error_filter, error_filter_length)
d = diff.all_diffs(haplotype.data, id1, id2, hap1_type=hap1_type, hap2_type=hap2_type)[0]
# Segment length, as defined by the input parameters
segment_length = lambda f: np.inf if not length_bound else (f.length if length_bound == 'base_pair' else f.num_snps) # @UnusedVariable
# Consider informative or the specified SNPs only
snps = snps if snps is not None else haplotype.snp_range
snps = np.intersect1d(snps, np.where(d != INDETERMINATE)[0])
d_snps = d[snps]
filtered_diff = filter_diff(d_snps, error_filter, error_filter_length)
error_snps = snps[np.nonzero(d_snps - filtered_diff)[0]]
# Detect edges as non-zero gradient points; output sufficiently long segments
bp = haplotype.snp['base_pair']
num_snps = haplotype.num_snps
if np.size(filtered_diff) == 0:
# No data to consider ==> no IBD intervals can be identified
segments = []
else:
deriv = ndimage.convolve(filtered_diff, [1, -1])
edge = np.where(deriv != 0)[0]
initial_phase = hap1_type if filtered_diff[0] == 0 else 1 - hap1_type
if debug:
print 'initial_phase', initial_phase # , 'edge', edge
# Convert recombination locations to segments of no recombination; filter short segments
segments = [f for f in (Segment(((x[0], x[1])), set(((id1, x[2]), (id2, hap2_type))),
(bp[x[0]], segment.stop_bp(bp, x[1], num_snps)),
error_snps=segment.in_segment(error_snps, x))
for x in segment.edges_to_segments(snps, edge, initial_phase,
haplotype.num_snps, hap1_type))
if segment_length(f) >= min_segment_length]
# Cut segment margins
if margin >= constants.SMALL_FLOAT:
segments = [s for s in (s.middle_part(haplotype.nearest_snp, bp, margin) for s in segments) if s]
# Restrict errors to those inside segments
segment_set = SegmentSet(segments,
np.array(util.flattened_meshgrid(reduce(list.__add__, (s.error_snps.tolist() for s in segments)),
np.array([id1, id2])), dtype=int) \
if segments else gt.empty_errors_array())
if debug:
print 'ibs_segments()', segment_set
print 'errors', segment_set.errors
return segment_set
