def test_reorder(self):
out_dict = str_and_dict.unify_freq_dicts(
self.freq_dicts,
key_separator="-",
)
#original
assert out_dict["WT"]["GLU30-LYS40"] == 1.0
assert out_dict["WT"]["GLU30-LYS50"] == .5
assert out_dict["WT"]["GLU30-LYS60"] == .1
assert "LYS60-GLU30" not in out_dict["WT"].keys() #bc reordering
#external
assert out_dict["WT"]["ALA40-GLU30"] == 0 #from K40A
assert out_dict["WT"]["GLH30-LYS40"] == 0 #from prot, reordered
# original
assert out_dict["K40A"]["ALA40-GLU30"] == .7
assert out_dict["K40A"]["GLU30-LYS60"] == .2 #was reordered
assert "LYS60-GLU30" not in out_dict["K40A"].keys()
# external
assert out_dict["K40A"]["GLU30-LYS40"] == 0 #from WT
assert out_dict["K40A"]["GLU30-LYS50"] == 0 #from WT
assert out_dict["K40A"]["GLH30-LYS40"] == 0 #from prot, reordered
# original
assert out_dict["prot"]["GLH30-LYS40"] == .3 #was reordered
assert "LYS40-GLH30" not in out_dict["prot"].keys()
# external
assert out_dict["prot"]["GLU30-LYS40"] == 0 # from WT
assert out_dict["prot"]["GLU30-LYS50"] == 0 # from WT
assert out_dict["prot"]["GLU30-LYS60"] == 0 # from WT, reordered
assert "LYS60-GLU30" not in out_dict["prot"].keys()
#assert out_dict["prot"]["LYS60-GLU30"] == 0 # from K40A not anymore, was set to 0 already
assert out_dict["prot"]["ALA40-GLU30"] == 0 # from K40A
def test_mutations(self):
out_dict = str_and_dict.unify_freq_dicts(
self.freq_dicts,
key_separator=None,
replacement_dict={"ALA40": "LYS40"})
#original
assert out_dict["WT"]["GLU30-LYS40"] == 1.0
assert out_dict["WT"]["GLU30-LYS50"] == .5
assert out_dict["WT"]["LYS60-GLU30"] == .1
#external
assert "ALA40-GLU30" not in out_dict["WT"].keys(
) #from K40A, will be now LYS40
assert out_dict["WT"][
"LYS40-GLU30"] == 0 #from K40A, was mutated back to LYS
assert out_dict["WT"]["GLU30-LYS60"] == 0 #from K40A
assert out_dict["WT"]["LYS40-GLH30"] == 0 #from prot
# original
assert out_dict["K40A"]["LYS40-GLU30"] == .7 #was mutated
assert out_dict["K40A"]["GLU30-LYS60"] == .2
# external
assert out_dict["K40A"]["GLU30-LYS40"] == 0 #from WT
assert out_dict["K40A"]["GLU30-LYS50"] == 0 #from WT
assert out_dict["K40A"]["LYS40-GLH30"] == 0 #from prot
# original
assert out_dict["prot"]["LYS40-GLH30"] == .3
# external
assert out_dict["prot"]["GLU30-LYS40"] == 0 # from WT
assert out_dict["prot"]["GLU30-LYS50"] == 0 # from WT
assert out_dict["prot"]["LYS60-GLU30"] == 0 # from WT
assert out_dict["prot"]["LYS60-GLU30"] == 0 # from K40A
assert out_dict["prot"]["LYS40-GLU30"] == 0 # from K40A
def test_basic_defrag(self):
out_dict = str_and_dict.unify_freq_dicts(self.freq_dicts,
key_separator=None,
defrag="@")
#original
assert out_dict["WT"]["GLU30-LYS40"] == 1.0
assert out_dict["WT"]["GLU30-LYS50"] == .5
assert out_dict["WT"]["LYS60-GLU30"] == .1
#external
assert out_dict["WT"]["ALA40-GLU30"] == 0 #from K40A
assert out_dict["WT"]["GLU30-LYS60"] == 0 #from K40A
assert out_dict["WT"]["LYS40-GLH30"] == 0 #from prot
# original
assert out_dict["K40A"]["ALA40-GLU30"] == .7
assert out_dict["K40A"]["GLU30-LYS60"] == .2
# external
assert out_dict["K40A"]["GLU30-LYS40"] == 0 #from WT
assert out_dict["K40A"]["GLU30-LYS50"] == 0 #from WT
assert out_dict["K40A"]["LYS40-GLH30"] == 0 #from prot
# original
assert out_dict["prot"]["LYS40-GLH30"] == .3
# external
assert out_dict["prot"]["GLU30-LYS40"] == 0 # from WT
assert out_dict["prot"]["GLU30-LYS50"] == 0 # from WT
assert out_dict["prot"]["LYS60-GLU30"] == 0 # from WT
assert out_dict["prot"]["LYS60-GLU30"] == 0 # from K40A
assert out_dict["prot"]["ALA40-GLU30"] == 0 # from K40A
def test_basic_exclude(self):
with pytest.raises(NotImplementedError):
out_dict = str_and_dict.unify_freq_dicts(
self.freq_dicts,
exclude=[
"LYS6"
], #to check that is just a pattern matching, not full str match
key_separator=None)
"""
def test_per_residue(self):
"""
self.freq_dicts = {"WT": {"GLU30-LYS40":1.0,
"GLU30-LYS50":.5,
"LYS60-GLU30": .1},
"K40A": {"ALA40-GLU30":.7,
"GLU30-LYS60": .2},
"prot": {"LYS40-GLH30": .3
}}
Returns
-------
"""
out_dict = str_and_dict.unify_freq_dicts(self.freq_dicts,
per_residue=True)
test_dict = {
"WT": {
"GLU30": 1.0 + .5 + .1,
"LYS40": 1.0 + 0,
"LYS50": .5,
"LYS60": .1,
"ALA40": 0,
"GLH30": 0
},
"K40A": {
"ALA40": .7,
"GLU30": .7 + .2,
"LYS60": .2,
"LYS40": 0,
"LYS50": 0,
"GLH30": 0
},
"prot": {
"GLU30": 0,
"LYS40": .3,
"LYS50": 0,
"LYS60": 0,
"ALA40": 0,
"GLH30": .3
}
}
self.assertDictEqual(out_dict["WT"], test_dict["WT"])
self.assertDictEqual(out_dict["K40A"], test_dict["K40A"])
self.assertDictEqual(out_dict["prot"], test_dict["prot"])