Common Denominator Helper
GitHub Link to Code.
Common denominator helper for feature selection system.
This module provides utilities for finding features that are present across all trajectories using biological feature identity comparison.
- class mdxplain.feature_selection.helper.common_denominator_helper.CommonDenominatorHelper
Helper class for common denominator operations in feature selection.
- static apply_common_denominator(pipeline_data: PipelineData, feature_key: str, trajectory_results: Dict[int, Any]) Dict[int, Any]
Apply common denominator filtering to keep only features present in all trajectories.
Uses biological feature identity (aaa_code, seqid, consensus) for comparison.
Parameters
- pipeline_dataPipelineData
Pipeline data object
- feature_keystr
Feature key
- trajectory_resultsdict
Dictionary with trajectory-specific indices
Returns
- dict
Filtered trajectory_results containing only common features
- static filter_using_identities(indices: List[int], use_reduced_flags: List[bool], trajectory_identities: List[dict], common_identities: List[dict]) tuple
Filter indices using pre-computed identities.
Parameters
- indicesList[int]
Original indices
- use_reduced_flagsList[bool]
Use reduced flags
- trajectory_identitiesList[dict]
Pre-computed feature identities for this trajectory
- common_identitiesList[dict]
Common feature identities to keep
Returns
- tuple
Tuple of (filtered_indices, filtered_use_reduced)
- static extract_feature_identities(pipeline_data: PipelineData, feature_key: str, traj_idx: int, indices: List[int], use_reduced_flags: List[bool]) List[Dict[str, Any]]
Extract biological feature identities for given indices.
Parameters
- pipeline_dataPipelineData
Pipeline data object
- feature_keystr
Feature key
- traj_idxint
Trajectory index
- indicesList[int]
Feature indices
- use_reduced_flagsList[bool]
Whether each index uses reduced data
Returns
- List[dict]
List of feature identities with biological information
- static find_common_feature_identities(trajectory_identities: dict) List[dict]
Find feature identities that are present in all trajectories.
Parameters
- trajectory_identitiesdict
Dictionary mapping trajectory indices to their feature identities
Returns
- List[dict]
List of feature identities common to all trajectories
- static filter_to_common_features(pipeline_data: PipelineData, feature_key: str, traj_idx: int, indices: List[int], use_reduced_flags: List[bool], common_identities: List[Dict[str, Any]]) Tuple[List[int], List[bool]]
Filter indices to keep only those matching common identities.
Parameters
- pipeline_dataPipelineData
Pipeline data object
- feature_keystr
Feature key
- traj_idxint
Trajectory index
- indicesList[int]
Original indices
- use_reduced_flagsList[bool]
Use reduced flags
- common_identitiesList[dict]
Common feature identities to keep
Returns
- tuple
Tuple of (filtered_indices, filtered_use_reduced)
- static identity_present_in_list(target_identity: dict, identity_list: List[dict]) bool
Check if target identity is present in identity list.
Parameters
- target_identitydict
Identity to search for (with “partners” key containing all partner info)
- identity_listList[dict]
List of identities to search in
Returns
- bool
True if identity is found (matches all partners’ aaa_code, seqid, consensus)