Read specialized bioinformatic file formats into dataframes.

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Project description

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

API Documentation

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

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0.3.1

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