Utilities for BiocPy

Motivation

This repository contains a variety of simple utilities for the BiocPy project, mostly convenient aspects of R that aren't provided by base Python. The aim is to simplify development of higher-level packages like scranpy and singler that would otherwise have to implement these methods individually.

Available utilities

match

import biocutils
biocutils.match(["A", "C", "E"], ["A", "B", "C", "D", "E"])
## [0, 2, 4]

factor

import biocutils
biocutils.factorize(["A", "B", "B", "A", "C", "D", "C", "D"])
## (['A', 'B', 'C', 'D'], [0, 1, 1, 0, 2, 3, 2, 3])

intersect

import biocutils
biocutils.intersect(["A", "B", "C", "D"], ["D", "A", "E"])
## ['A', 'D']

union

import biocutils
biocutils.union(["A", "B", "C", "D"], ["D", "A", "E"])
## ['A', 'B', 'C', 'D', 'E']

subset

import biocutils
biocutils.subset(["A", "B", "C", "D", "E"], [0, 2, 4])
## ['A', 'C', 'E']

import numpy as np
y = np.array([10, 20, 30, 40, 50])
biocutils.subset(y, [0, 2, 4])
## array([10, 30, 50])

is_list_of_type

Checks if all elements of a list or tuple are of the same type.

import biocutils
import numpy as np

x = [np.random.rand(3), np.random.rand(3, 2)]
biocutils.is_list_of_type(x, np.ndarray)
## True

and many more. Check out the documentation for more information.