msmu._read_write._base_reader

MuDataInput dataclass

MuDataInput(raw_feature_df, norm_feature_df, norm_quant_df, search_config, decoy_df)

Dataclass to store inputs for creating a MuData object.

Attributes:

Name	Type	Description
raw_feature_df	DataFrame	Raw feature DataFrame (varm['search_result']).
norm_feature_df	DataFrame	Normalized feature DataFrame.
norm_quant_df	DataFrame	Normalized quantification DataFrame.
search_result	DataFrame	Original search result DataFrame.
search_config	dict	Configuration settings from the search engine.

SearchResultReader

SearchResultReader()

Base class for reading and processing search engine results.

Attributes:

Name	Type	Description
search_settings	SearchResultSettings	Settings for the search results.
used_feature_cols	list[str]	List of columns to be used in the feature DataFrame.
base_level	Literal['psm', 'precursor'] | None	Base level of the data (e.g., "psm" or "precursor").
_feature_rename_dict	dict	Dictionary for renaming feature columns.

Methods:

Name	Description
read	Reads and processes the search results into a MuData object.

read

read()

Reads and processes the search results into a MuData object.

Returns:

Type	Description
MuData	md.MuData: A MuData object containing the processed search results.

SearchResultSettings dataclass

SearchResultSettings(search_engine, quantification, label, acquisition, output_dir, feature_file, feature_level, quantification_file, quantification_level, config_file, feat_quant_merged, has_decoy=True)

Dataclass to store search result settings.

Attributes:

Name	Type	Description
search_engine	str	Name of the search engine used (e.g., "sage", "maxquant").
quantification	str | None	Name of the quantification tool used (e.g., "sage", "maxquant", or None).
label	str	Labeling method used (e.g., "tmt", "label_free").
output_dir	Path	Directory where the search results are stored.
feature_file	str	Name of the feature file.
feature_level	str	Level of the feature data (e.g., "psm", "precursor", "peptide", "protein").
quantification_file	str | None	Name of the quantification file (if applicable).
quantification_level	str | None	Level of the quantification data (e.g., "psm", "precursor", "peptide", "protein", or None).
config_file	str | None	Name of the configuration file (if applicable).
feat_quant_merged	bool	Indicates if feature and quantification are merged in a single file.

config_path property

config_path

Returns the full path to the configuration file if it exists, otherwise returns None.

feature_path property

feature_path

Returns the full path to the feature file if it exists, otherwise returns None.

quantification_path property

quantification_path

Returns the full path to the quantification file if it exists, otherwise returns None.