def __init__(self,
file_location,
analyzer='Unknown',
instrument_label='Unknown'):
"""
# Parameters
----------
file_location: text, pathlib.Path(), or s3path.S3Path
Path object from pathlib containing the file location
"""
if isinstance(file_location, str):
# if obj is a string it defaults to create a Path obj, pass the S3Path if needed
file_location = Path(file_location)
if not file_location.exists():
raise FileNotFoundError("%s not found" % file_location)
if not file_location.suffix == '.corems':
raise TypeError("%s is not a valid CoreMS file" % file_location)
Thread.__init__(self)
ReadCoremsMasslist.__init__(self, file_location)
self.lcms = LCMSBase(self.file_location,
analyzer=analyzer,
instrument_label=instrument_label)
def test_import_corems_mass_list():
file_location = Path.cwd() / "tests/tests_data/ESI_NEG_SRFA_COREMS.csv"
#polarity need to be set or read from the file
#load any type of mass list file, change the delimeter to read another type of file, i.e : "," for csv, "\t" for tabulated mass list, etc
mass_list_reader = ReadCoremsMasslist(file_location, analyzer='ICR', instrument_label='12T')
mass_spectrum = mass_list_reader.get_mass_spectrum()
for mspeak in mass_spectrum:
if mspeak:
for mf in mspeak:
print(mf.string)
file_location = Path.cwd() / "tests/tests_data/" / "NEG_ESI_SRFA_CoreMS.corems"
read_lc_ms = ReadCoremsMassSpectraText(file_location)
read_lc_ms.start()
read_lc_ms.join()
mass_spectra = read_lc_ms.get_lcms_obj()
for mspeak in mass_spectra[0]:
if mspeak:
for mf in mspeak:
print('mass_spectra', mf.string)
def import_corems_mass_list():
file_location = Path.cwd() / "tests/tests_data/" / "ESI_NEG_SRFA_COREMS.csv"
#polarity need to be set or read from the file
#load any type of mass list file, change the delimeter to read another type of file, i.e : "," for csv, "\t" for tabulated mass list, etc
mass_list_reader = ReadCoremsMasslist(file_location)
mass_spectrum = mass_list_reader.get_mass_spectrum()
return mass_spectrum
def __init__(self, file_location, analyzer='Unknown', instrument_label='Unknown'):
if not Path(file_location).exists:
raise FileNotFoundError("%s not found" % file_location)
if not Path(file_location).suffix == '.corems':
raise TypeError("%s is not a valid CoreMS file" % file_location)
Thread.__init__(self)
ReadCoremsMasslist.__init__(self, file_location)
self.lcms = LCMSBase(self.file_location, analyzer=analyzer,instrument_label=instrument_label)