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 0.2.16

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 0.2.16
File	Size	Uploaded
BiocFrame-0.2.16.tar.gz	27.5 kB	Aug 16, 2023	Details

Built distribution (wheel)

Table of built distributions (wheels) for biocframe 0.2.16
File	Interpreter	ABI	Platform	Reset
BiocFrame-0.2.16-py3-none-any.whl 12.2 kB Aug 16, 2023	Python 3	none	any	Details

Total release size: 39.7 kB

Release files / BiocFrame-0.2.16.tar.gz

Download URL	BiocFrame-0.2.16.tar.gz
Size	27.5 kB
Tags	Source
SHA-256 checksum How to use checksums	`702474cbc53c01aeb5a38415623943e3ecd6273dcc23d0482817a6709af22862`
BLAKE2b-256 checksum How to use checksums	`d1652656e01c04ef00363b87982876f3f4cd4fc3d3810cf9362b1adbe1f372aa`
Upload date	Aug 16, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.17`

Release files / BiocFrame-0.2.16-py3-none-any.whl

Download URL	BiocFrame-0.2.16-py3-none-any.whl
Size	12.2 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`3505d96f9d48481dbcd9662e2d65fe60f99b592afd55d2fc7d2656353f492c0d`
BLAKE2b-256 checksum How to use checksums	`215c61068b84b19079c536270ab43ab452eca173587bb3a253ca0da8cd6e0f84`
Upload date	Aug 16, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.17`