def test_map_mod_chemical_composition():
mapper = UnimodMapper()
mod_list = [
{
"aa":
"M", # specify the modified amino acid as a single letter, use '*' if the amino acid is variable
"type":
"opt", # specify if it is a fixed (fix) or potential (opt) modification
"position":
"any", # specify the position within the protein/peptide (Prot-N-term, Prot-C-term), use 'any' if the positon is variable
"name":
"Oxidation", # specify the unimod PSI-MS Name (alternative to id)
"id": None, # specify the unimod Accession (alternative to name)
"composition":
None, # For user-defined mods composition needs to be given as a Hill notation
},
{
"aa": "T",
"type": "fix",
"name": "Acetyl",
},
]
rdict = mapper.map_mods(mod_list)
assert rdict["opt"][0]["composition"] == {"O": 1}
assert rdict["fix"][0]["composition"] == {"C": 2, "H": 2, "O": 1}
assert rdict["fix"][0]["id"] == "1"
def test_map_mod_chemical_composition_fails():
mapper = UnimodMapper()
# Using PSI-MS name works
mod_list = [
{
"aa": "N",
"type": "opt",
"name": "Ammonia-loss",
},
]
rdict = mapper.map_mods(mod_list)
assert rdict["opt"][0]["name"] == "Ammonia-loss"
# Using Interim name for same ID doesn't work
mod_list = [
{
"aa": "D",
"type": "opt",
"name": "N-oxobutanoic",
},
]
rdict = mapper.map_mods(mod_list)
assert len(rdict["opt"]) == 0
# Using Interim name and ID doesn't work (cause name is checked first)
# But using a wrong ID but correct name works (see test_map_mods_name_and_wrong_id)
# Seems inconsistent
mod_list = [
{
"aa": "D",
"type": "opt",
"name": "N-oxobutanoic",
"id": 385,
},
]
rdict = mapper.map_mods(mod_list)
assert len(rdict["opt"]) == 0
# Using just ID works
mod_list = [
{
"aa": "D",
"type": "opt",
"id": 385,
},
]
rdict = mapper.map_mods(mod_list)
assert rdict["opt"][0]["name"] == "Ammonia-loss"
# Using Interim name if PSI MS name doesn't exist works
mod_list = [
{
"aa": "S",
"type": "opt",
"name": "Galactosyl",
},
]
rdict = mapper.map_mods(mod_list)
assert rdict["opt"][0]["composition"] == {"C": 6, "H": 10, "O": 6}
def test_map_mod_userdefined_compositions():
mapper = UnimodMapper()
mod_list = [
{
"aa":
"M", # specify the modified amino acid as a single letter, use '*' if the amino acid is variable
"type":
"opt", # specify if it is a fixed (fix) or potential (opt) modification
"position":
"any", # specify the position within the protein/peptide (Prot-N-term, Prot-C-term), use 'any' if the positon is variable
"name":
"TheOneAndOnly", # specify the unimod PSI-MS Name (alternative to id)
"composition": {
"H": 2,
"O": 1,
}, # For user-defined mods composition needs to be given as a Hill notation
},
]
rdict = mapper.map_mods(mod_list)
assert (
len(rdict["opt"]) == 0
) # cause the name is not a unimod mod, but the composition exists already
mod_list = [
{
"aa":
"M", # specify the modified amino acid as a single letter, use '*' if the amino acid is variable
"type":
"opt", # specify if it is a fixed (fix) or potential (opt) modification
"position":
"any", # specify the position within the protein/peptide (Prot-N-term, Prot-C-term), use 'any' if the positon is variable
"name":
"TheOneAndOnly", # specify the unimod PSI-MS Name (alternative to id)
"composition": {
"H": 222,
"O": 111,
}, # For user-defined mods composition needs to be given as a Hill notation
},
]
rdict = mapper.map_mods(mod_list)
assert rdict["opt"][0]["composition"] == {"H": 222, "O": 111}
assert rdict["opt"][0]["name"] == "TheOneAndOnly"
def test_map_mods_neutral_loss():
import pprint
pprint.pprint(mod_dict_nl["parameters"]["modifications"])
_output = UnimodMapper().map_mods(
mod_list=mod_dict_nl["parameters"]["modifications"])
print("Output")
pprint.pprint(_output)
print("Expected")
pprint.pprint(unimod_dict_with_nl)
assert _output == unimod_dict_with_nl
def test_map_composition_to_ids():
mapper = UnimodMapper()
mapped = mapper.composition_to_ids({"C": 1, "O": 1})
assert list(mapped) == ["122", "1196", "1205"]
def test_map_composition_to_names():
mapper = UnimodMapper()
mapped = mapper.composition_to_names({"C": 1, "O": 1})
assert list(mapped) == ["Formyl", "Ser->Asp", "Thr->Glu"]
def test_map_TMTpro18():
mapper = UnimodMapper()
mapped = mapper.mass_to_names(304.207146,
decimals=4) # starts working from 3 on
assert list(mapped) == ["TMTpro"]
def test_map_mods_name_and_wrong_id():
_output = UnimodMapper().map_mods(
mod_list=mod_dict_name_wrong_id["parameters"]["modifications"])
assert _output == unimod_dict_name_wrong_id
def test_map_mods_mod_not_in_unimod_by_id():
_output = UnimodMapper().map_mods(
mod_list=mod_dict_id_not_in_unimod["parameters"]["modifications"])
assert _output == {"fix": [], "opt": []}
def test_map_mods_by_name():
_output = UnimodMapper().map_mods(
mod_list=mod_dict["parameters"]["modifications"])
assert _output == unimod_dict