Unit tests

BiocFrame

This package provides a data frame representation similar to a pandas DataFrame, with support for nested column types.

Install

Package is published to PyPI

pip install biocframe

Usage

Lets create a BiocFrame from a dictionary

from random import random
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.column_names)

Setters

Using the Pythonic way to set properties

# set new column names
bframe.column_names = [..., new_column_names, ...]
print(bframe.column_names)

# 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 4.5. For details and usage information on PyScaffold see https://pyscaffold.org/.

Release files for biocframe 0.3.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for biocframe 0.3.0
File	Size	Uploaded
BiocFrame-0.3.0.tar.gz	29.3 kB	Aug 20, 2023	Details

Built distribution (wheel)

Table of built distributions (wheels) for biocframe 0.3.0
File	Interpreter	ABI	Platform	Reset
BiocFrame-0.3.0-py3-none-any.whl 13.0 kB Aug 20, 2023	Python 3	none	any	Details

Total release size: 42.3 kB

Release files / BiocFrame-0.3.0.tar.gz

Download URL	BiocFrame-0.3.0.tar.gz
Size	29.3 kB
Tags	Source
SHA-256 checksum How to use checksums	`2dad7da77164a692f9b7f3df84f6461a85d8e429d31814a8bffcea8670467dd3`
BLAKE2b-256 checksum How to use checksums	`c910e5ed53f29deb0d9fa122c252bfb163fb00588721974ba3ba32d9dfce425f`
Upload date	Aug 20, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.17`

Release files / BiocFrame-0.3.0-py3-none-any.whl

Download URL	BiocFrame-0.3.0-py3-none-any.whl
Size	13.0 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`7653bea8ea7f16696ee33054e4781d5030d5926c646b586b19111dcf4d9d53ac`
BLAKE2b-256 checksum How to use checksums	`4528a55f5409ac8e8f25fe2ece0669a7f2c1a5430cb9ac4e2e70ef868c94f86e`
Upload date	Aug 20, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.17`