BiocFrame 0.2.9

BiocFrame class to support complex types in Genomics. The goal is to not compete with `Pandas` but be inter-operable at some point.

BiocFrame

BiocFrame provides a base BiocFrame class, intended to be a flexible data structure compared to Pandas DataFrame This would be interoperable with pandas but will support usecases in genomics.

Install

Package is published to PyPI

pip install biocframe

Usage

Lets create a BiocFrame from a dictionary

from biocframe import BiocFrame

bframe = BiocFrame(
    data = {
        "seqnames": [
            "chr1",
            "chr2",
            "chr2",
            "chr2",
            "chr1",
            "chr1",
            "chr3",
            "chr3",
            "chr3",
            "chr3",
        ]
        * 20,
        "starts": range(100, 300),
        "ends": range(110, 310),
        "strand": ["-", "+", "+", "*", "*", "+", "+", "+", "-", "-"] * 20,
        "score": range(0, 200),
        "GC": [random() for _ in range(10)] * 20,
    }
)

Access Properties

Accessor methods/properties are available to access column names, row names and dims.

# find the dimensions
print(bframe.dims)

# get the column names
print(bframe.columnNames)

Setters

Using the Pythonic way to set properties

# set new column names
bframe.columnNames = [... new colnames ...]
print(bframe.columnNames)

# add or reassign columns

bframe["score"] = range(200, 400)

Slice the BiocFrame

Currently slicing is only supported by indices or names (column names or row names). A future version may implement pandas query like operations.

sliced_bframe = bframe[3:7, 2:5]

For more use cases including subset, checkout the documentation

Note

This project has been set up using PyScaffold 4.3. For details and usage information on PyScaffold see https://pyscaffold.org/.