alphabase.scoring.feature_extraction_base

Classes:

BaseFeatureExtractor()

class alphabase.scoring.feature_extraction_base.BaseFeatureExtractor

Bases: object

Methods:

__init__()
extract_features(psm_df, *args, **kwargs)	Extract the scoring features (self._feature_list) and append them inplace into candidate PSMs (psm_df).
update_features(psm_df)	This method allow us to update adaptive features during the iteration of Percolator algorithm

Attributes:

feature_list

This is a property.

__init__()

extract_features(psm_df: DataFrame, *args, **kwargs) → DataFrame

Extract the scoring features (self._feature_list) and append them inplace into candidate PSMs (psm_df).

All sub-classes must re-implement this method.

Parameters:

psm_df (pd.DataFrame) – PSMs to be rescored

Returns:

psm_df with appended feature columns extracted by this extractor

Return type:

pd.DataFrame

property feature_list: list

This is a property. It tells ML scoring modules what features (columns) are extracted by this FeatureExtractor for scoring.

Returns:

feature names (columns) in the PSM dataframe

Return type:

list

update_features(psm_df: DataFrame) → DataFrame

This method allow us to update adaptive features during the iteration of Percolator algorithm

Parameters:

psm_df (pd.DataFrame) – psm_df

Returns:

psm_df with updated feature values

Return type:

pd.DataFrame