Source code for matchms.filtering.add_precursor_mz

import logging
from matchms.utils import get_first_common_element

logger = logging.getLogger("matchms")

_default_key = "precursor_mz"
_accepted_keys = ["precursormz", "precursor_mass"]
_accepted_types = (float, str, int)
_accepted_missing_entries = ["", "N/A", "NA", "n/a"]

[docs]def add_precursor_mz(spectrum_in): """Add precursor_mz to correct field and make it a float. For missing precursor_mz field: check if there is "pepmass"" entry instead. For string parsed as precursor_mz: convert to float. """ if spectrum_in is None: return None spectrum = spectrum_in.clone() metadata_updated = _add_precursor_mz_metadata(spectrum.metadata) spectrum.metadata = metadata_updated return spectrum
def _convert_precursor_mz(precursor_mz): """Convert precursor_mz to number if possible. Otherwise return None.""" if precursor_mz is None: return None if isinstance(precursor_mz, str) and precursor_mz in _accepted_missing_entries: return None if not isinstance(precursor_mz, _accepted_types): logger.warning("Found precursor_mz of undefined type.") return None if isinstance(precursor_mz, str): try: return float(precursor_mz.strip()) except ValueError: logger.warning("%s can't be converted to float.", precursor_mz) return None return precursor_mz def _add_precursor_mz_metadata(metadata): precursor_mz_key = get_first_common_element([_default_key] + _accepted_keys, metadata.keys()) precursor_mz = metadata.get(precursor_mz_key) precursor_mz = _convert_precursor_mz(precursor_mz) if isinstance(precursor_mz, (float, int)): metadata["precursor_mz"] = float(precursor_mz) for key in _accepted_keys: metadata.pop(key, None) return metadata pepmass = metadata.get("pepmass", None) if pepmass is not None and _convert_precursor_mz(pepmass[0]) is not None: metadata["precursor_mz"] = pepmass[0] logger.warning("Added precursor_mz entry based on field 'pepmass'." "Consider running 'interpret_pepmass() filter first.") return metadata logger.warning("No precursor_mz found in metadata.") metadata.pop("precursor_mz", None) return metadata