def test_EstimateDistances_fromUnaligned(self):
"""Excercising estimate distances from unaligned sequences"""
d = EstimateDistances(self.collection,
JC69(),
do_pair_align=True,
rigorous_align=True)
d.run(show_progress=False)
canned_result = {
("b", "e"): 0.440840,
("c", "e"): 0.440840,
("a", "c"): 0.088337,
("a", "b"): 0.188486,
("a", "e"): 0.440840,
("b", "c"): 0.0883373,
}
result = d.get_pairwise_distances().to_dict()
self.assertDistsAlmostEqual(canned_result, result)
d = EstimateDistances(self.collection,
JC69(),
do_pair_align=True,
rigorous_align=False)
d.run(show_progress=False)
canned_result = {
("b", "e"): 0.440840,
("c", "e"): 0.440840,
("a", "c"): 0.088337,
("a", "b"): 0.188486,
("a", "e"): 0.440840,
("b", "c"): 0.0883373,
}
result = d.get_pairwise_distances().to_dict()
self.assertDistsAlmostEqual(canned_result, result)
def test_EstimateDistances_fromThreeway(self):
"""testing (well, exercising at least), EsimateDistances fromThreeway"""
d = EstimateDistances(self.al, JC69(), threeway=True)
d.run(show_progress=False)
canned_result = {
("b", "e"): 0.495312,
("c", "e"): 0.479380,
("a", "c"): 0.089934,
("a", "b"): 0.190021,
("a", "e"): 0.495305,
("b", "c"): 0.0899339,
}
result = d.get_pairwise_distances(summary_function="mean").to_dict()
self.assertDistsAlmostEqual(canned_result, result)
def test_EstimateDistances(self):
"""testing (well, exercising at least), EstimateDistances"""
d = EstimateDistances(self.al, JC69())
d.run(show_progress=False)
canned_result = {
("b", "e"): 0.440840,
("c", "e"): 0.440840,
("a", "c"): 0.088337,
("a", "b"): 0.188486,
("a", "e"): 0.440840,
("b", "c"): 0.0883373,
}
result = d.get_pairwise_distances().to_dict()
self.assertDistsAlmostEqual(canned_result, result)
# excercise writing to file
d.write("junk.txt")
try:
os.remove("junk.txt")
except OSError:
pass # probably parallel