def test_pick_3_prime_set_of_deletions_and_substitutions():
# set of deletions should slide to the end
a = Polymorphism(27,0,'T')
b = Polymorphism(29,0,'T')
c = Polymorphism(33,0,'-')
d = Polymorphism(30,0,'T')
e = Polymorphism(33,0,'C')
f = Polymorphism(27,0,'-')
input = [[a,b,c],[d,e,f]]
output = [[a,b,c]]
result = prefer_indels_at_end(input)
for x in result:
x.sort()
assert output == prefer_indels_at_end(input)
def test_pick_most_3_prime_single_deletion():
# alternates are two contiguous deletions
a = Polymorphism(1,0,'-')
b = Polymorphism(2,0,'-')
input = [[a], [b]]
output = [[b]]
assert output == prefer_indels_at_end(input)
def test_pick_3_prime_set_of_deletions():
# set of deletions should slide to the end
a = Polymorphism(1,0,'-')
b = Polymorphism(2,0,'-')
c = Polymorphism(3,0,'-')
d = Polymorphism(4,0,'-')
e = Polymorphism(2,0,'-')
f = Polymorphism(3,0,'-')
g = Polymorphism(4,0,'-')
h = Polymorphism(5,0,'-')
input = [[a,b,c,d],[e,f,g,h]]
output = [[e,f,g,h]]
result = prefer_indels_at_end(input)
for x in result:
x.sort()
assert output == prefer_indels_at_end(input)
def test_that_multiple_deletions_in_an_alignment_are_not_lost():
# two deletions in a row in the same alt_aln should not be reduced
a = Polymorphism(1,0,'-')
b = Polymorphism(2,0,'-')
input = [[a,b]]
output = [[a,b]]
assert output == prefer_indels_at_end(input)
def test_pick_most_3_prime_pair_of_insertions():
# alternates are two contiguous insertions, with a shared site
a = Polymorphism(1,1,'A')
b = Polymorphism(5,0,'A')
c = Polymorphism(2,1,'A')
d = Polymorphism(5,0,'A')
input = [[a,b], [c,d]]
output = [[c,d]]
assert output == prefer_indels_at_end(input)
def test_pick_most_3_prime_deletion_carrying_a_substitution():
# alternates are two contiguous deletions, with a shared site
a = Polymorphism(1,0,'-')
b = Polymorphism(2,0,'-')
c = Polymorphism(5,0,'A')
d = Polymorphism(5,0,'A')
input = [[a,c], [b,d]]
output = [[b,d]]
assert output == prefer_indels_at_end(input)
def test_pick_most_3_prime_of_many_single_deletions():
# alternates are several contiguous deletions
a = Polymorphism(1,0,'-')
b = Polymorphism(2,0,'-')
c = Polymorphism(3,0,'-')
d = Polymorphism(4,0,'-')
e = Polymorphism(5,0,'-')
input = [[a], [e], [b], [c], [d]]
output = [[e]]
assert output == prefer_indels_at_end(input)
def test_pick_most_3_prime_insertion():
# alternates are several contiguous insertions
a = Polymorphism(1,1,'A')
b = Polymorphism(2,1,'A')
c = Polymorphism(3,1,'A')
d = Polymorphism(4,1,'A')
e = Polymorphism(5,1,'A')
input = [[a], [e], [b], [c], [d]]
output = [[e]]
assert output == prefer_indels_at_end(input)
def test_pick_most_3_prime_set_of_insertions():
# triplets of multi-inserts
a = Polymorphism(1,1,'A')
b = Polymorphism(1,2,'A')
c = Polymorphism(5,1,'A')
d = Polymorphism(2,1,'A')
e = Polymorphism(2,2,'A')
f = Polymorphism(6,1,'A')
input = [[a,b,c],[d,e,f]]
output = [[d,e,f]]
assert output == prefer_indels_at_end(input)
def test_pick_most_3_prime_double_insertion():
# pairs of multi-inserts
a = Polymorphism(1,1,'A')
b = Polymorphism(1,2,'A')
c = Polymorphism(2,1,'A')
d = Polymorphism(2,2,'A')
e = Polymorphism(3,1,'A')
f = Polymorphism(3,2,'A')
input = [[a,b],[c,d],[e,f]]
output = [[e,f]]
assert output == prefer_indels_at_end(input)
def test_pick_most_3_prime_pair_of_separated_insertions():
# alternates are two near, but not contiguous pairs
a = Polymorphism(1,1,'A')
b = Polymorphism(2,1,'A')
c = Polymorphism(2,1,'A')
d = Polymorphism(3,1,'A')
input = [[a,b],[c,d]]
output = [[c,d]]
result = prefer_indels_at_end(input)
for x in result:
x.sort()
assert output == result
def test_pick_3_prime_pair_of_deletions():
# paired deletions should slide to the end
a = Polymorphism(1,0,'-')
b = Polymorphism(2,0,'-')
c = Polymorphism(2,0,'-')
d = Polymorphism(3,0,'-')
input = [[a,b],[c,d]]
output = [[c,d]]
result = prefer_indels_at_end(input)
for x in result:
x.sort()
assert output == result
def test_most_3_prime_matched_pair_of_deletions():
# alternates are 2 pairs of 2 contiguous deletions
a = Polymorphism(1,0,'-')
b = Polymorphism(2,0,'-')
c = Polymorphism(20,0,'-')
d = Polymorphism(21,0,'-')
e = Polymorphism(1,0,'-')
f = Polymorphism(2,0,'-')
g = Polymorphism(20,0,'-')
h = Polymorphism(21,0,'-')
input = [[a,c], [e,d], [b,g], [f,h]]
output = [[f,h]]
assert output == prefer_indels_at_end(input)
def test_pick_most_3_prime_pair_of_deletions_from_many():
# alternates are 2 pairs of contiguous deletions
# one is a choice among 2, the other is a choice among 3
a = Polymorphism(1,0,'-')
b = Polymorphism(20,0,'-')
c = Polymorphism(1,0,'-')
d = Polymorphism(21,0,'-')
e = Polymorphism(2,0,'-')
f = Polymorphism(20,0,'-')
g = Polymorphism(2,0,'-')
h = Polymorphism(21,0,'-')
i = Polymorphism(3,0,'-')
j = Polymorphism(20,0,'-')
k = Polymorphism(3,0,'-')
l = Polymorphism(21,0,'-')
input = [[a,b], [c,d], [e,f], [g,h], [i,j], [k,l]]
output = [[k,l]]
assert output == prefer_indels_at_end(input)
def test_two_consecutive_insertions():
a = Polymorphism(1,1,'A')
b = Polymorphism(2,1,'A')
input = [[a], [b]]
output = [[b]]
assert output == prefer_indels_at_end(input)