def test_intervals_to_array():
from pydigree.sgs.sgs import intervals_to_array
intervals = [[2, 4], [6, 10]]
observed = intervals_to_array(intervals, 15)
expected = np.array([0, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0])
assert all(observed == expected)
assert all(intervals_to_array([], 10) == np.zeros(10))
def test_intervals_to_array():
from pydigree.sgs.sgs import intervals_to_array
intervals = [[2,4], [6,10] ]
observed = intervals_to_array(intervals, 15)
expected = np.array([0, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0])
assert all(observed==expected)
assert all(intervals_to_array([], 10) == np.zeros(10))
replicate = sys.argv[1]
ms = int(sys.argv[2])
prefix='null'
peds = pyd.io.plink.read_plink('{}-{}.ped'.format(prefix, replicate), '{}.map'.format(prefix))
ped = peds['1']
s = pyd.sgs.sgs_population(ped, seed_size=ms)
with smartopen('{}-{}.ibd.gz'.format(prefix, replicate)) as f:
trueibd = {}
for line in f:
fam, id1, id2, ibd_states = line.strip().split(None, 3)
trueibd[frozenset({id1,id2})] = np.array([int(x) for x in ibd_states.split()])
a = intervals_to_array(s[frozenset({ped['7'],ped['8']})][0], ped.chromosomes[0].nmark())
b = trueibd[frozenset({'7','8'})]
genos1 = zip(*ped['7'].genotypes[0])
genos2 = zip(*ped['8'].genotypes[0])
identical = [ibs(x,y) for x,y in zip(genos1, genos2)]
from pydigree.common import table, runs
for start, stop in runs(list(a), lambda x: x>0, ms):
print('Predicted segment: {}-{}'.format(start, stop))
print()