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/.

Release files for biocframe 0.2.15

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 0.2.15
File	Size	Uploaded
BiocFrame-0.2.15.tar.gz	27.4 kB	Jul 23, 2023	Details

Built distribution (wheel)

Table of built distributions (wheels) for biocframe 0.2.15
File	Interpreter	ABI	Platform	Reset
BiocFrame-0.2.15-py3-none-any.whl 12.2 kB Jul 23, 2023	Python 3	none	any	Details

Total release size: 39.6 kB

Release files / BiocFrame-0.2.15.tar.gz

Download URL	BiocFrame-0.2.15.tar.gz
Size	27.4 kB
Tags	Source
SHA-256 checksum How to use checksums	`a0611723ad14887acab1e453799c054055afac814776ffda0d1c110e3d1cb4a4`
BLAKE2b-256 checksum How to use checksums	`a8459c88bbc3ca850dd3ee9776913233755756b2f0c20f5a59fdc01b51bb3946`
Upload date	Jul 23, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.17`

Release files / BiocFrame-0.2.15-py3-none-any.whl

Download URL	BiocFrame-0.2.15-py3-none-any.whl
Size	12.2 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`e86682a9362a101807289fc8371af4b28c0787972b3eb8cf7449b9f0fb0a3c24`
BLAKE2b-256 checksum How to use checksums	`814d1353750905558b731fa8a9d3763181a0c29557016acb8ff7152152661912`
Upload date	Jul 23, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.17`