Python _filled_members Examples

Example #1

File: TestIbdGermline1Restricted.py Project: orenlivne/ober

 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())

Example #2

 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())

Example #3

File: TestIbdGermline1.py Project: orenlivne/ober

 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())

Example #4

 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())

Example #5

 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())

Example #6

File: TestIbdGermline2Small.py Project: orenlivne/ober

 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())

Example #7

            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)