def test_mt1_mt3_disagree_3p_alt_cut(self,
mt1_yes_seed_shifted_yes_3p_alt_cut,
mt3_yes_seed_shifted_no_3p_alt_cut):
d = ModificationThing.disagreements([
mt1_yes_seed_shifted_yes_3p_alt_cut,
mt3_yes_seed_shifted_no_3p_alt_cut])
assert d == ('is_3p_alt_cut',)
def test_mt1_mt3_disagree_3p_alt_cut(self,
mt1_yes_seed_shifted_yes_3p_alt_cut,
mt3_yes_seed_shifted_no_3p_alt_cut):
d = ModificationThing.disagreements([
mt1_yes_seed_shifted_yes_3p_alt_cut,
mt3_yes_seed_shifted_no_3p_alt_cut
])
assert d == ('is_3p_alt_cut', )
def test_other_edited_n17_and_3p_mismatch_with_seed_shift_ex_21b_minus(
self, main_hit_B_, ex_21b_):
m = ModificationThing(main_hit_B_, ex_21b_)
assert m.is_other_edited
assert m.is_3p_mismatch
assert m.is_seed_shifted
def test_other_edited_n17_with_seed_shift_ex_20b(self, main_hit_B, ex_20b):
m = ModificationThing(main_hit_B, ex_20b)
assert m.is_other_edited
assert not m.is_3p_mismatch
assert m.is_seed_shifted
def test_3p_mismatch_with_seed_shift_ex_9b_minus(self, main_hit_B_,
ex_9b_):
m = ModificationThing(main_hit_B_, ex_9b_)
assert m.is_3p_mismatch
assert m.is_seed_shifted
assert not m.is_3p_alt_cut
def test_3p_alt_cut_with_seed_shift_ex_7b(self, main_hit_B, ex_7b):
m = ModificationThing(main_hit_B, ex_7b)
assert m.is_3p_alt_cut
assert m.is_seed_shifted
assert not m.is_3p_mismatch
def test_mismatches_coords_ex_2(self, main_hit_A, ex_2):
m = ModificationThing(main_hit_A, ex_2)
assert (11, 16, 17) == m._mismatches_coords(main_hit_A, ex_2)
def test_mt2_mt2_no_disagree(self, mt2_no_seed_shifted_yes_3p_alt_cut):
d = ModificationThing.disagreements([
mt2_no_seed_shifted_yes_3p_alt_cut,
mt2_no_seed_shifted_yes_3p_alt_cut
])
assert d == ()
def mt1_yes_seed_shifted_yes_3p_alt_cut(
self, main_hit_B, hit_yes_seed_shifted_yes_3p_alt_cut):
return ModificationThing(main_hit_B,
hit_yes_seed_shifted_yes_3p_alt_cut)
def test_mismatches_coords_ex_2_minus(self, main_hit_A_, ex_2_):
m = ModificationThing(main_hit_A_, ex_2_)
assert (9, 14, 15) == m._mismatches_coords(main_hit_A_, ex_2_)
def test_mismatches_coords_ex_2(self, main_hit_A, ex_2):
m = ModificationThing(main_hit_A, ex_2)
assert (11, 16, 17) == m._mismatches_coords(main_hit_A, ex_2)
def test_mismatches_coords_ex_1_minus(self, main_hit_A_, ex_1_):
m = ModificationThing(main_hit_A_, ex_1_)
assert (0, 11, 16, 17) == m._mismatches_coords(main_hit_A_, ex_1_)
def test_mt2_mt2_no_disagree(self,
mt2_no_seed_shifted_yes_3p_alt_cut):
d = ModificationThing.disagreements([
mt2_no_seed_shifted_yes_3p_alt_cut,
mt2_no_seed_shifted_yes_3p_alt_cut])
assert d == ()
def test_mismatches_coords_ex_2_minus(self, main_hit_A_, ex_2_):
m = ModificationThing(main_hit_A_, ex_2_)
assert (9, 14, 15) == m._mismatches_coords(main_hit_A_, ex_2_)
def test_not_other_edited_n16_no_seed_shift_3p_mismatch_ex_23a(
self, main_hit_B, ex_23a):
m = ModificationThing(main_hit_B, ex_23a)
assert not m.is_other_edited
assert m.is_3p_mismatch
assert not m.is_seed_shifted
def test_not_other_edited_n16_seed_shift_3p_mismatch_ex_24b_minus(
self, main_hit_B_, ex_24b_):
m = ModificationThing(main_hit_B_, ex_24b_)
assert not m.is_other_edited
assert m.is_3p_mismatch
assert m.is_seed_shifted
def test_3p_mismatch_ex_4a(self, main_hit_B, ex_4a):
m = ModificationThing(main_hit_B, ex_4a)
assert m.is_3p_mismatch
assert not m.is_seed_shifted
assert not m.is_3p_alt_cut
def mt4_no_seed_shifted_no_3p_alt_cut(self, main_hit_B,
hit_no_seed_shifted_no_3p_alt_cut):
return ModificationThing(main_hit_B, hit_no_seed_shifted_no_3p_alt_cut)
def test_3p_mismatch_and_3p_alt_cut_ex_5d_minus(self, main_hit_B_, ex_5d_):
m = ModificationThing(main_hit_B_, ex_5d_)
assert m.is_3p_mismatch
assert m.is_3p_alt_cut
assert not m.is_seed_shifted
def test_3p_alt_cut_with_seed_shift_ex_7a_minus(self, main_hit_B_, ex_7a_):
# minus strand
m = ModificationThing(main_hit_B_, ex_7a_)
assert m.is_3p_alt_cut
assert m.is_seed_shifted
assert not m.is_3p_mismatch
def test_mismatches_coords_ex_1_minus(self, main_hit_A_, ex_1_):
m = ModificationThing(main_hit_A_, ex_1_)
assert (0, 11, 16, 17) == m._mismatches_coords(main_hit_A_, ex_1_)