Unit tests

BiocFrame

This package provides BiocFrame class, a dataframe-like representation similar to a pandas, with support for flexible and nested objects.

BiocFrame makes no assumption on the types of the columns, the minimum requirement is each column implements length: __len__ and slice: __getitem__ operations.

To get started, install the package from 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 0.3.12

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 0.3.12
File	Size	Uploaded
BiocFrame-0.3.12.tar.gz	31.1 kB	Oct 12, 2023	Details

Built distribution (wheel)

Table of built distributions (wheels) for biocframe 0.3.12
File	Interpreter	ABI	Platform	Reset
BiocFrame-0.3.12-py3-none-any.whl 13.8 kB Oct 12, 2023	Python 3	none	any	Details

Total release size: 44.8 kB

Release files / BiocFrame-0.3.12.tar.gz

Download URL	BiocFrame-0.3.12.tar.gz
Size	31.1 kB
Tags	Source
SHA-256 checksum How to use checksums	`814771120e1b77b762bc8b8569ffcf15d6eb2a4ec662197a0a1f01738012aac7`
BLAKE2b-256 checksum How to use checksums	`4bccdc22e6f6cf3359fc4e3dfed6af700506ef74a23136fbad545b3c65dcb6e1`
Upload date	Oct 12, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.18`

Release files / BiocFrame-0.3.12-py3-none-any.whl

Download URL	BiocFrame-0.3.12-py3-none-any.whl
Size	13.8 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`5133dd97e610d6a854b8fd44cbb3ef4c78ccecdc1d8110754fee020c79acdbff`
BLAKE2b-256 checksum How to use checksums	`7797b8d0026c51f65dbae5efa8b5d64052f128499474f754878de9726eba7c42`
Upload date	Oct 12, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.18`