Source code for phenotrex.util.helpers

#
# Created by Lukas Lüftinger on 14/02/2019.
#
from typing import List, Tuple

import numpy as np

from phenotrex.structure.records import TrainingRecord


[docs]def get_x_y_tn_ft(records: List[TrainingRecord]) -> Tuple[np.ndarray, np.ndarray, str, str]:
    """
    Get separate X and y from list of TrainingRecord.
    Also infer trait name from first TrainingRecord.

    :param records: a List[TrainingRecord]
    :return: separate lists of features and targets, the trait name and the feature type
    """
    trait_name = records[0].trait_name
    feature_type = records[0].feature_type
    X = np.array([" ".join(x.features) for x in records])
    y = np.array([x.trait_sign for x in records])
    return X, y, trait_name, feature_type


[docs]def get_groups(records: List[TrainingRecord]) -> np.ndarray:
    """
    Get groups from list of TrainingRecords

    :param records:
    :return: list for groups
    """
    group_ids = np.array([x.group_id for x in records])
    return group_ids


[docs]def fail_missing_dependency(*args, **kwargs):
    raise ImportError('FASTA file annotation requires the optional dependency deepnog. '
                      'Install with pip.')