Support package for Alevin tools. Updated and repackaged version of k3yavi/vpolo
Project description
fingerling
The output of salmon alevin
is a binary sparse matrix. fingerling
is a python module for reading that output into a pandas
dataframe suitable for downstream analysis.
Code is derived from k3yavi/vpolo
, updated to use maturin for Python/Rust integration.
Installation
Requirements:
fingerling
requires Python 3.10 (or greater) as well as:
pandas
numpy
scipy
Additionally, since fingerling contains a submodule written in Rust, a working installation of Rust is required. See instructions for installing Rust here.
Install fingerling from this repository using:
pip install git+https://github.com/milescsmith/fingerling
If you wish to download the source and build it locally, you will also need maturin
. Prior to installing the local files, you will need to run maturin build
followed by pip install .target/wheels/fingerling-X.X.X-cp3XX-cp3XX-OS_VERSION_PLATFORM.whl
, where X.X.X
corresponds to the package version, cp3XX
the python version, and OS_VERSION_PLATFORM
your operating system and version. The actual name and location for the wheel should be given by maturin
at the end of the build.
Basic Usage
Currently, fingerling
is not setup to be used as a standalone executable, but instead used as part of an analysis pipeline in something like a Jupyter notebook. The read_quants_bin
function returns a sample-by-feature dataframe with an index corresponding to the cell barcodes and column names corresponding to the feature names and is suitable for use in creating an AnnData
object:
import scanpy as sc
from fingerling import read_quants_bin
cite_df = read_quants_bin("/PATH/TO/ALEVIN_OUTPUT")
adata = sc.Anndata(X=cite_df)
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