def test_lipid_check_consistency():
l = Lipid(LipidClass('Cer'), ResidueList([Residue(16, 2), Residue(18, 1)]))
# check inconsistent state
assert l.residueslist[0].modification == None
l.check_consistency()
# check consistent state
assert l.residueslist[0].modification == CLASS_DEFAULT_MODIFICATION['Cer']
def some_lipids_plain_list():
"""
A handful of well formatted lipids, using all annotation elements.
Return as Python list, not as LipidList Object
"""
# lists of names to draw from
lipidclass_names = ['CE', 'Cer', 'TG']
modifications = ['d', 'O-', None, None]
lipidlist = []
for i in range(10):
lipidclass = LipidClass(random.choice(lipidclass_names))
num_of_residues = random.choice([1, 2, 3])
residuelist = ResidueList()
for i in range(0, num_of_residues):
residuelist.residues.append(
Residue(random.randint(6, 50),
random.randint(0, 10),
modification=ResidueModification(
random.choice(modifications))))
lipidlist.append(Lipid(lipidclass, residuelist))
return lipidlist
def test_lipidlist_append():
lipidlist = LipidList()
for i in range(10):
lipidlist.append(Lipid())
assert len(lipidlist) == 10
def test_lipid_xreflist():
t = 'DAG 16:0;0_22:4;0'
lipid = Lipid.parse(t)
lipid.add_xref(
Xref('TargetDB', 'targetid')
)
assert len(lipid.xreflist) == 1
def test_swisslipids_xref():
lipid = Lipid.parse('CE(20:2)')
lipid = SwissLipids.get_xrefs(lipid)
for xref in lipid.xreflist:
assert xref.target_db == SwissLipids.NAME
assert any(x.target_id == 'SLM:000500283' for x in lipid.xreflist)
def get_xrefs(cls, lipid: Lipid, summed: bool = False) -> XrefList:
xreflist = XrefList()
try:
search_term = lipid.abbreviation(summed)
except Exception as e:
log.debug(
f"No abbreviation for lipid: {lipid.lipidclass}, {lipid.residueslist}."
)
log.error(f"Failed with {e}")
search_term = lipid.abbreviation()
search_result = cls.run_search(search_term)
# search result can be empyt
if search_result:
for entity in cls.run_search(lipid.abbreviation(summed)):
xreflist.append(Xref(cls.NAME, entity['entity_id']))
return xreflist
def test_parse(self):
t = 'CE 16:2;0'
lipid = Lipid.parse(t)
assert lipid.lipidclass.name == 'CE'
assert lipid.residueslist[0].carbon_atoms == 16
assert lipid.residueslist[0].double_bonds == 2
assert lipid.residueslist[0].oxidation == 0
t = 'CE(16:2;0)'
lipid = Lipid.parse(t)
assert lipid.lipidclass.name == 'CE'
assert lipid.residueslist[0].carbon_atoms == 16
assert lipid.residueslist[0].double_bonds == 2
assert lipid.residueslist[0].oxidation == 0
t = 'DAG 16:0;0_22:4;0'
lipid = Lipid.parse(t)
assert lipid.lipidclass.name == 'DG'
assert len(lipid.residueslist) == 2
assert lipid.residueslist[0].carbon_atoms == 16
assert lipid.residueslist[0].double_bonds == 0
assert lipid.residueslist[0].oxidation == 0
t = 'PC(28:5(13Z,16Z,19Z,22Z,25Z)/0:0)'
lipid = Lipid.parse(t)
assert lipid.lipidclass.name == 'PC'
assert len(lipid.residueslist) == 2
assert lipid.residueslist[0].carbon_atoms == 28
assert lipid.residueslist[0].double_bonds == 5
assert lipid.residueslist[0].oxidation == None
assert len(lipid.residueslist[0].zstatelist) == 5
assert str(lipid.residueslist[0].zstatelist[1]) == '16Z'
t = 'chol'
lipid = Lipid.parse(t)
assert str(lipid.lipidclass) == 'chol'
def lipid_from_id(cls, swisslipidsid: str) -> Lipid:
"""
Call API to get details for a SwissLipids ID.
:param swisslipidsid: The SwissLipids ID.
:return: Return a Lipid.
"""
request_url = cls.BASE_URL + f'/entity/{swisslipidsid.strip()}'
log.debug(f'Call: {request_url}')
result = requests.get(request_url).json()
# get abbreviation
for synonym in result['synonyms']:
if synonym['type'] == 'abbreviation':
abbreviation = synonym['name']
lipid = Lipid.parse(abbreviation)
lipid.add_xref(Xref(cls.NAME, swisslipidsid))
return lipid
def test_lipid_abbreviation():
l = Lipid(LipidClass('CE'), ResidueList([Residue(16, 2)]))
assert l.abbreviation() == 'CE(16:2)'
l = Lipid(LipidClass('CE'), ResidueList([Residue(16, 2), Residue(18, 1)]))
assert l.abbreviation() == 'CE(16:2/18:1)'
assert l.abbreviation(summed=True) == 'CE(34:3)'
l = Lipid(LipidClass('CE'), ResidueList([Residue(16, 2, modification=ResidueModification('O-')), Residue(18, 1)]))
assert l.abbreviation() == 'CE(O-16:2/18:1)'
assert l.abbreviation(summed=True) == 'CE(O-34:3)'
# no residues, assure that abbreviation/summed fails with AttributeError
l = Lipid(LipidClass('CE'))
assert l.abbreviation() == 'CE'
assert l.abbreviation(summed=True) == 'CE'
def test_errors(self):
with pytest.raises(TypeError):
# string not ending with bracket
Lipid.parse("CE(14:9(9Z)/8:0")