phenotrex.transforms package

Submodules

phenotrex.transforms.annotation module

phenotrex.transforms.resampling module

class phenotrex.transforms.resampling.TrainingRecordResampler(random_state: Optional[float] = None, verb: bool = False)

Bases: object

Instantiates an object which can generate versions of a TrainingRecord resampled to defined completeness and contamination levels. Requires prior fitting with full List[TrainingRecord] to get sources of contamination for both classes.

Parameters

• random_state – Randomness seed to use while resampling

• verb – Toggle verbosity

fit(records: List[phenotrex.structure.records.TrainingRecord])

Fit TrainingRecordResampler on full TrainingRecord list to determine set of positive and negative features for contamination resampling.

Parameters

records – the full List[TrainingRecord] on which ml training will commence.

Returns

True if fitting was performed, else False.

get_resampled(record: phenotrex.structure.records.TrainingRecord, comple: float = 1.0, conta: float = 0.0) → phenotrex.structure.records.TrainingRecord

Resample a TrainingRecord to defined completeness and contamination levels. Comple=1, Conta=1 will double set size.

Parameters

• comple – completeness of returned TrainingRecord features. Range: 0 - 1

• conta – contamination of returned TrainingRecord features. Range: 0 - 1

• record – the input TrainingRecord

Returns

a resampled TrainingRecord.

Module contents

phenotrex.transforms.fastas_to_grs(*args, **kwargs)