py-oxbow

py-oxbow

A Python interface for oxbow. Read specialized bioinformatic file formats into dataframes.

Installation

Warning: oxbow is new and under active development. It is not yet ready for production as APIs are subject to change.

pip install oxbow

Usage

import oxbow as ox

arrow_ipc = ox.read_bam("data.bam", "chr1:1-100000")

# Read into polars
import polars as pl
df = pl.read_ipc(arrow_ipc)

# Read into pandas
import io
import pyarrow.ipc
df = pyarrow.ipc.open_file(io.BytesIO(ipc)).read_pandas()

Development

This project uses maturin and hatch for development, which can be installed with pipx.

# create a virtual env
hatch shell

# compile a development version of the package
maturin develop --release

# open the jupyter notebooks/
jupyterlab

A local build of oxbow will be added to your virtual environment.

import oxbow as ox