BiocFrame 0.2.16

lite weight data frame class that supports nestes structures.

BiocFrame

This package implements a lite weight data frame like class (comparable to Pandas DataFrame) but supports more flexible column types, e.g: nested columns.

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/.