sercol

sercol provides Collection, a sequence that filters and groups while keeping its collection type and source metadata, and saves to JSON through serializable. It is the base class for varcode's VariantCollection and EffectCollection and mhctools' BindingPredictionCollection, so their filtering and grouping behave the same.

Install

python -m pip install sercol

Python 3.11 or later is required; pip installs serializable and pandas 3.

Filter and group values

from sercol import Collection

values = Collection([5, 2, 3, 2])
selected = values.filter(lambda value: value >= 3)
groups = values.groupby(lambda value: value % 2)
print(list(selected))
print({key: list(group) for key, group in groups.items()})

[5, 3]
{1: [5, 3], 0: [2, 2]}

filter() returns a collection; groupby() returns a dictionary of collections. Both keep the original collection class and its distinct, sort_key and sources. The original collection is unchanged.

Save and reload

Continuing with values above:

restored = Collection.from_json(values.to_json())
print(list(restored))
print(restored == values)

[5, 2, 3, 2]
True

Serialization uses serializable. Elements and constructor state must be supported by that format. A sort_key must be a function defined at the top level of a module, so that it can be imported when reconstructing the collection; to_json() raises ValueError for a lambda or a function defined inside another function.

See select, order and track values for thresholds, multiple grouping keys and source metadata. The API reference lists all collection operations.