Module epiclass.utils.metadata_utils
Metadata analysis basic utility functions. Also defines some constants.
Functions
def count_combinations(my_metadata: Metadata, categories: Iterable[str], use_uuid: bool = False) ‑> Counter[Tuple[str, ...]]-
Return label combinations counter from the given metadata categories.
Args
my_metadata:Metadata- Experiment metadata to analyze.
categories:List[str]- A list of categories to count.
use_uuid:bool- If True, count combinations by uuid; otherwise, by md5sum.
Returns
Counter (Tuple[str, …], int): A counter object that counts label combinations.
def count_labels_from_dset(dset: KnownData, label_category: str, from_uuid)-
Returns a Counter object containing the counts of all examples of a given label category in a dataset.
This function processes the dataset and organizes the samples by the specified label category, counting the number of occurrences for each unique label.
Args
dset:KnownData- The dataset object containing the samples and metadata.
label_category:str- The specific label category to count (e.g., "assay", "cell_type").
from_uuid:bool- A flag to determine whether to use "uuid" or "md5sum" as the identifying label.
Returns
collections.Counter- A Counter object with the unique labels as keys and the counts as values.
def count_pairs(my_metadata: Metadata, cat1: str, cat2: str, use_uuid: bool = False) ‑> Counter[Tuple[str, str]]-
Return label pairs (label_cat1, label_cat2) counter from the given metadata categories.
Args
my_metadata:Metadata- experiment metadata to analyze.
cat1:str- The first category to count.
cat2:str- The second category to count.
use_uuid:bool- If True, count pairs by uuid; otherwise, by md5sum.
Returns
Counter (Tuple[str, str], int): A counter object that counts label pairs.
def make_table(my_metadata: Metadata, cat1: str, cat2: str, filepath: str)-
Write metadata content tsv table for given metadata categories
def print_pairs(my_metadata: Metadata, cat1: str, cat2: str)-
Print label pairs from the given metadata categories.