def test_lipid_fragment_fail(self):
goslin_parser = Parser(GoslinParserEventHandler(), "pygoslin/data/goslin/Goslin.g4", ParserTest.PARSER_QUOTE)
lipid_name = "PE 16:1-12:0 - -(H20)"
lipid = goslin_parser.parse(lipid_name)
assert lipid != None
def test_lipid_fragment_fail(self):
file_name = os.path.join("pygoslin", "data", "goslin", "Goslin.g4")
goslin_parser = Parser(GoslinParserEventHandler(), file_name,
ParserTest.PARSER_QUOTE)
lipid_name = "PE 16:1-12:0 - -(H20)"
lipid = goslin_parser.parse(lipid_name)
assert lipid != None
def test_adduct(self):
goslin_parser_event_handler = GoslinParserEventHandler()
goslin_parser = Parser(goslin_parser_event_handler, "pygoslin/data/goslin/Goslin.g4")
lipid_name = "PE 16:1/12:0[M+H]1+"
lipid = goslin_parser.parse(lipid_name)
assert lipid != None
assert lipid.get_lipid_string() == "PE 16:1/12:0[M+H]1+"
def test_adduct(self):
goslin_parser_event_handler = GoslinParserEventHandler()
file_name = os.path.join("pygoslin", "data", "goslin", "Goslin.g4")
goslin_parser = Parser(goslin_parser_event_handler, file_name)
lipid_name = "PE 16:1/12:0[M+H]1+"
lipid = goslin_parser.parse(lipid_name)
assert lipid != None
assert lipid.get_lipid_string() == "PE 16:1/12:0[M+H]1+"
def test_lipid_names(self):
file_name = os.path.join("pygoslin", "data", "goslin", "Goslin.g4")
goslin_parser = Parser(GoslinParserEventHandler(), file_name,
ParserTest.PARSER_QUOTE)
## glycerophospholipid
lipid_name = "PE 16:1/12:0"
lipid = goslin_parser.parse(lipid_name)
assert lipid != None
assert lipid.lipid.get_lipid_string(
LipidLevel.STRUCTURAL_SUBSPECIES) == "PE 16:1/12:0"
assert lipid.lipid.get_lipid_string(
LipidLevel.MOLECULAR_SUBSPECIES) == "PE 16:1-12:0"
assert lipid.lipid.get_lipid_string(LipidLevel.SPECIES) == "PE 28:1"
assert lipid.lipid.get_lipid_string(LipidLevel.CLASS) == "PE"
assert lipid.lipid.get_lipid_string(LipidLevel.CATEGORY) == "GP"
## sphingolipid
lipid_name = "Cer 16:1;2/12:0"
lipid = goslin_parser.parse(lipid_name)
assert lipid != None
assert lipid.lipid.get_lipid_string(
LipidLevel.STRUCTURAL_SUBSPECIES) == "Cer 16:1;2/12:0"
assert lipid.lipid.get_lipid_string(
LipidLevel.MOLECULAR_SUBSPECIES) == "Cer 16:1;2-12:0"
assert lipid.lipid.get_lipid_string(LipidLevel.SPECIES) == "Cer 28:1;2"
assert lipid.lipid.get_lipid_string(LipidLevel.CLASS) == "Cer"
assert lipid.lipid.get_lipid_string(LipidLevel.CATEGORY) == "SP"
## glycerolipid
lipid_name = "TAG 16:1/12:0/20:2"
lipid = goslin_parser.parse(lipid_name)
assert lipid != None
assert lipid.lipid.get_lipid_string(
LipidLevel.STRUCTURAL_SUBSPECIES) == "TAG 16:1/12:0/20:2"
assert lipid.lipid.get_lipid_string(
LipidLevel.MOLECULAR_SUBSPECIES) == "TAG 16:1-12:0-20:2"
assert lipid.lipid.get_lipid_string(LipidLevel.SPECIES) == "TAG 48:3"
assert lipid.lipid.get_lipid_string(LipidLevel.CLASS) == "TAG"
assert lipid.lipid.get_lipid_string(LipidLevel.CATEGORY) == "GL"
## sterol
lipid_name = "ChE 16:1"
lipid = goslin_parser.parse(lipid_name)
assert lipid != None
assert lipid.lipid.get_lipid_string(
LipidLevel.STRUCTURAL_SUBSPECIES) == "SE 27:1/16:1"
assert lipid.lipid.get_lipid_string(
LipidLevel.MOLECULAR_SUBSPECIES) == "SE 27:1/16:1"
assert lipid.lipid.get_lipid_string(
LipidLevel.SPECIES) == "SE 27:1/16:1"
assert lipid.lipid.get_lipid_string(LipidLevel.CLASS) == "SE 27:1"
assert lipid.lipid.get_lipid_string(LipidLevel.CATEGORY) == "ST"
## sterol
lipid_name = "SE 27:1/16:1"
lipid = goslin_parser.parse(lipid_name)
assert lipid != None
assert lipid.lipid.get_lipid_string(
LipidLevel.STRUCTURAL_SUBSPECIES) == "SE 27:1/16:1"
assert lipid.lipid.get_lipid_string(
LipidLevel.MOLECULAR_SUBSPECIES) == "SE 27:1/16:1"
assert lipid.lipid.get_lipid_string(
LipidLevel.SPECIES) == "SE 27:1/16:1"
assert lipid.lipid.get_lipid_string(LipidLevel.CLASS) == "SE 27:1"
assert lipid.lipid.get_lipid_string(LipidLevel.CATEGORY) == "ST"
## PC
lipid_name = "PC O-18:1a/16:0"
lipid = goslin_parser.parse(lipid_name)
assert lipid != None
assert lipid.lipid.get_lipid_string(
LipidLevel.STRUCTURAL_SUBSPECIES) == "PC O-18:1a/16:0"
assert lipid.lipid.get_lipid_string(
LipidLevel.MOLECULAR_SUBSPECIES) == "PC O-18:1a-16:0"
assert lipid.lipid.get_lipid_string(LipidLevel.SPECIES) == "PC O-34:1a"
assert lipid.lipid.get_lipid_string(LipidLevel.CLASS) == "PC"
assert lipid.lipid.get_lipid_string(LipidLevel.CATEGORY) == "GP"
def __init__(self):
self.event_handler = GoslinParserEventHandler()
dir_name = path.dirname(pygoslin.__file__)
file_name = path.join(dir_name, "data", "goslin", "Goslin.g4")
super().__init__(self.event_handler, file_name, Parser.DEFAULT_QUOTE)
def __init__(self):
self.event_handler = GoslinParserEventHandler()
dir_name = path.dirname(pygoslin.__file__)
super().__init__(self.event_handler,
dir_name + "/data/goslin/Goslin.g4",
Parser.DEFAULT_QUOTE)