massdash.loaders.MzMLDataLoader

class massdash.loaders.MzMLDataLoader(**kwargs)

Bases: GenericSpectrumLoader

Class to load data from MzMLFiles using a .osw output file or .tsv report file

rsltsFile

(str) The path to the report file (DIANN-TSV or OSW)

dataFiles

(str/List[str]) The path to the mzML file(s)

libraryFile

(str) The path to the library file (.tsv or .pqp)

loadFeatureMaps(pep_id: str, charge: int, config=<class 'massdash.structs.TargetedDIAConfig.TargetedDIAConfig'>, runNames: None | str | ~typing.List[str] = None) → FeatureMapCollection

Loads a dictionary of FeatureMaps (where the keys are the filenames) from the results file

Parameters:

  • pep_id (str) – Peptide ID

  • charge (int) – Charge

  • runNames (None | str | List[str]) – Name of the run to extract the feature map from. If None, all runs are extracted. If str, only the specified run is extracted. If List[str], only the specified runs are extracted.

Returns:

FeatureMapCollection containing FeatureMap objects for each file

Return type:

FeatureMapCollection

loadTransitionGroups(pep_id: str, charge: int, config: TargetedDIAConfig, runNames: None | str | List[str] = None) → Dict[str, TransitionGroup]

Loads the transition group for a given peptide ID and charge across all files

Parameters:

  • pep_id (str) – Peptide ID

  • charge (int) – Charge

  • config (TargetedDIAConfig) – Configuration object containing the extraction parameters

  • runNames (None | str | List[str]) – Name of the run to extract the transition group from. If None, all runs are extracted. If str, only the specified run is extracted. If List[str], only the specified runs are extracted.

Returns:

Dictionary of TransitionGroups, with keys as filenames

Return type:

dict[str, TransitionGroup]

loadTransitionGroupsDf(pep_id: str, charge: int, config: TargetedDIAConfig) → Dict[str, DataFrame]

Loads the transition group for a given peptide ID and charge across all files into a pandas DataFrame

Parameters:

  • pep_id (str) – Peptide ID

  • charge (int) – Charge

  • config (TargetedDIAConfig) – Configuration object containing the extraction parameters

Returns:

Dictionary of TransitionGroups, with keys as filenames

Return type:

dict[str, pd.DataFrame]