def test_load_from_mzxml():
"""Test parsing of mzxml file to spectrum objects"""
module_root = os.path.dirname(__file__)
mzxml_file = os.path.join(module_root, "testdata.mzXML")
spectrum = next(load_from_mzxml(mzxml_file))
assert len(list(
load_from_mzxml(mzxml_file))) == 1, "Expected single spectrum"
assert int(spectrum.get(
"precursor_mz")) == 343, "Expected different precursor m/z"
assert spectrum.get("charge") == -1, "Expected different charge."
assert len(spectrum.peaks) == 50
def convert_files_to_matchms_spectrum_objects(
file_name) -> Union[List[Spectrum], None]:
"""Loads spectra from your spectrum file into memory as matchms Spectrum object
The following file extensions can be loaded in with this function:
"mzML", "json", "mgf", "msp", "mzxml", "usi" and "pickle".
A pickled file is expected to directly contain a list of matchms spectrum objects.
Args:
-----
file_name:
Path to file containing spectra, with file extension "mzML", "json", "mgf", "msp",
"mzxml", "usi" or "pickle"
"""
assert os.path.exists(
file_name), f"The specified file: {file_name} does not exists"
file_extension = os.path.splitext(file_name)[1].lower()
if file_extension == ".mzml":
return list(importing.load_from_mzml(file_name))
if file_extension == ".json":
return list(importing.load_from_json(file_name))
if file_extension == ".mgf":
return list(importing.load_from_mgf(file_name))
if file_extension == ".msp":
return list(importing.load_from_msp(file_name))
if file_extension == ".mzxml":
return list(importing.load_from_mzxml(file_name))
if file_extension == ".usi":
return list(importing.load_from_usi(file_name))
if file_extension == ".pickle":
return load_pickled_file(file_name)
print(f"File extension of file: {file_name} is not recognized")
return None
def test_load_from_mzxml_ms_levels():
"""Test parsing of mzxml file to spectrum objects using different ms levels."""
module_root = os.path.dirname(__file__)
mzxml_file = os.path.join(module_root, "testdata.mzXML")
expected_num_spectra = [1, 1, 3, 0]
for i in range(4):
ms_level = i + 1
spectrums = list(load_from_mzxml(mzxml_file, ms_level))
assert len(spectrums) == expected_num_spectra[i], (
f"Expected different number of spectrums for ms_level={ms_level}")