phenotrex.util package

Submodules

phenotrex.util.helpers module

phenotrex.util.helpers.fail_missing_dependency(*args, **kwargs)

phenotrex.util.helpers.get_groups(records: List[phenotrex.structure.records.TrainingRecord]) → numpy.ndarray

Get groups from list of TrainingRecords

Parameters

records –

Returns

list for groups

phenotrex.util.helpers.get_x_y_tn_ft(records: List[phenotrex.structure.records.TrainingRecord]) → Tuple[numpy.ndarray, numpy.ndarray, str, str]

Get separate X and y from list of TrainingRecord. Also infer trait name from first TrainingRecord.

Parameters

records – a List[TrainingRecord]

Returns

separate lists of features and targets, the trait name and the feature type

phenotrex.util.logging module

phenotrex.util.logging.get_logger(initname, verb=False)

This function provides a logger to all scripts used in this project.

Parameters

• initname – The name of the logger to show up in log.

• verb – Toggle verbosity

Returns

the finished Logger object.

phenotrex.util.plotting module

phenotrex.util.taxonomy module

Module contents