Read Seurat .rds and .h5seurat file to anndata object. Implemented in pure python.
Project description
readseurat
Read Seurat .rds and .h5seurat files into AnnData — implemented in pure Python, no R required.
The code for rds parsing is based on the rdata package (https://github.com/vnmabus/rdata).
Installation
pip install readseurat
Python API
import readseurat
# Read an RDS file containing a Seurat object
adata = readseurat.read_seurat("pbmc3k.rds")
# Read an H5Seurat file
adata = readseurat.read_h5seurat("pbmc3k.h5seurat")
Commandline
Convert a Seurat file to H5AD format:
# From RDS
readseurat convert pbmc3k.rds pbmc3k.h5ad
# From H5Seurat
readseurat convert pbmc3k.h5seurat pbmc3k.h5ad
Usage: readseurat convert [OPTIONS] INPUT OUTPUT
Convert a Seurat file (RDS or H5Seurat) to H5AD format.
Options:
--format [rds|h5seurat] Input file format. Inferred from file extension if
not specified.
-h, --help Show this message and exit.
Citation
rdata package:
Ramos-Carreño, C., & Rossi, T. (2024). rdata: A Python library for R datasets. Journal of Open Source Software, 9(104), 1–4. https://doi.org/10.21105/joss.07540
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file readseurat-0.1.0.tar.gz.
File metadata
- Download URL: readseurat-0.1.0.tar.gz
- Upload date:
- Size: 36.3 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: uv/0.10.10 {"installer":{"name":"uv","version":"0.10.10","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
b44be0dc5c685a3028c7bdcde563409d0cd05e0a951aaac79e39e7a5d1218abb
|
|
| MD5 |
77b5c2a60500419542c97c7eb2749f93
|
|
| BLAKE2b-256 |
8a643c2cfd229520cfa1ab28d181d7d3c3138f83843bae2027a14eb5735278b3
|
File details
Details for the file readseurat-0.1.0-py3-none-any.whl.
File metadata
- Download URL: readseurat-0.1.0-py3-none-any.whl
- Upload date:
- Size: 44.9 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: uv/0.10.10 {"installer":{"name":"uv","version":"0.10.10","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
7afda1630fe2d0f695f5b1d04506d8096de4be05980a99bccb78e65a1b7974c4
|
|
| MD5 |
104c17f9abbcadf47804e5dd121505ef
|
|
| BLAKE2b-256 |
94f02cdd16294d7f4e2d368ad54b09b586510a93c26f6902482cf846954ee8fb
|
