BiocFrame

BiocFrame provides a base BiocFrame class, intended to be a flexible data structure compared to Pandas DataFrame This would be interoperable with pandas but will support usecases in genomics.

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 0.2.9

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 0.2.9
File	Size	Uploaded
BiocFrame-0.2.9.tar.gz	26.5 kB	Mar 23, 2023	Details

Built distribution (wheel)

Table of built distributions (wheels) for biocframe 0.2.9
File	Interpreter	ABI	Platform	Reset
BiocFrame-0.2.9-py3-none-any.whl 10.6 kB Mar 23, 2023	Python 3	none	any	Details

Total release size: 37.2 kB

Release files / BiocFrame-0.2.9.tar.gz

Download URL	BiocFrame-0.2.9.tar.gz
Size	26.5 kB
Tags	Source
SHA-256 checksum How to use checksums	`6694221efe26b532aafac082a9f7d7c6b8a9ad04fd72b8871248bb3c554ed017`
BLAKE2b-256 checksum How to use checksums	`44a3a9a3957b7f3ceaa5a7b276e49a8405126472a71799eb214ae1f0209cc180`
Upload date	Mar 23, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.16`

Release files / BiocFrame-0.2.9-py3-none-any.whl

Download URL	BiocFrame-0.2.9-py3-none-any.whl
Size	10.6 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`d50957e23c6b96860c21e96284ca2603969b3923ff50b7fc5ab0fbf93ffdf9fd`
BLAKE2b-256 checksum How to use checksums	`fa9f1e54e48b7b0162463764bf14574110d906600885338c3c73046ef41bd6ee`
Upload date	Mar 23, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.16`