def setUp(self):
'''Load single nuclear family test case.'''
# Remove a key child to make problem more interesting for the IBD algorithm
self.problem = im.io.read_npz(itu.FAMILY945_ONE_PARENT_STAGE2).remove_nodes([2])
self.family = self.problem.families(genotyped=False)[0]
self.sibs = ig._filled_members(self.problem, self.family)
self.ibd_computer = ig.GermlineIbdComputer(PhaseParam())
def setUp(self):
'''Load single nuclear family test case.'''
# Remove a key child to make problem more interesting for the IBD algorithm
self.problem = im.io.read_npz(
itu.FAMILY945_ONE_PARENT_STAGE2).remove_nodes([2])
self.family = self.problem.families(genotyped=False)[0]
self.sibs = ig._filled_members(self.problem, self.family)
self.ibd_computer = ig.GermlineIbdComputer(PhaseParam())
def setUp(self):
'''Load single nuclear family test case.'''
self.problem = im.io.read_npz(itu.FAMILY945_ONE_PARENT_STAGE2)
self.family = self.problem.families(genotyped=False)[0]
self.sibs = ig._filled_members(self.problem, self.family)
self.ibd_computer = ig.GermlineIbdComputer(PhaseParam())
def setUp(self):
'''Load single nuclear family test case.'''
self.problem = im.io.read_npz(itu.SIB_FOUNDERS_STAGE3)
self.family = self.problem.families(genotyped=False)[0]
self.sibs = ig._filled_members(self.problem, self.family)
self.ibd_computer = ig.GermlineIbdComputer(PhaseParam())
def setUp(self):
'''Load single nuclear family test case.'''
self.problem = im.io.read_npz(itu.FAMILY4_STAGE3)
self.family = self.problem.first_family
self.sibs = ig._filled_members(self.problem, self.family)
self.ibd_computer = ig.GermlineIbdComputer(PhaseParam())
def setUp(self):
'''Load single nuclear family test case.'''
self.problem = im.io.read_npz(itu.FAMILY4_STAGE3)
self.family = self.problem.first_family
self.sibs = ig._filled_members(self.problem, self.family)
self.ibd_computer = ig.GermlineIbdComputer(PhaseParam())
ibd.append(set([remaining]))
return d
def longest_segment(d):
return max([(snp, len(ibd)) for (snp,ibd) in d.iteritems()], key=operator.itemgetter(1))
def hash_ibd_list(ibd):
return dict(((sample, i) for (i, samples) in enumerate(ibd) for sample in samples))
def highest_degree_node(ibd):
return max([(i,len(ibd[hap_index[(i,0)]])+len(ibd[hap_index[(i,1)]])) for i in sibs],
key=operator.itemgetter(1))[0]
p = im.io.read_npz(itu.SIB_FOUNDERS_STAGE3)
f = p.families(genotyped=False)[0]
sibs = ig._filled_members(p, f)
h_mat = ig._HapMatrix(p, sibs)
print h_mat
c = ig.GermlineIbdComputer()
segments = c.ibd_segments(h_mat)
segments.group_to_disjoint()
print segments
haps = set(itertools.product(sibs, ALLELES))
d = compress(segments, haps)
(best_segment, num_haps) = longest_segment(d)
print best_segment, num_haps
ibd = d[best_segment]
print ibd
hap_index = hash_ibd_list(ibd)
template = highest_degree_node(ibd)
