adview

Adview: Anndata Viewer: head/less/view adata(h5ad) files in yout terminal.

Why adview

Are you still doing this?:

❯ python3
Python 3.13.2 (main, Feb  4 2025, 14:51:09) [Clang 16.0.0 (clang-1600.0.26.6)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import scanpy as sc   ## hold on, be patient with your HPC🚬
>>> adata = sc.read_h5ad('path/to/adata.h5ad')
>>> adata.var
>>> adata.obs
>>> adata.shape

I just want to glance！👀

Now, let adview comfort you!

Installation

git clone https://github.com/JianYang-Lab/adview.git
cd adview
cargo build --release
./target/release/adview -h

or just

cargo install --git https://github.com/JianYang-Lab/adview.git
adview -h

Usage

❯ adview -h
adview -- Adata Viewer: Head/Less/Shape h5ad file in terminal

Version: 0.1.0

Authors: wenjiewei<[email protected]>

Usage: adview <COMMAND>

Commands:
  obs-head  Show first n obs [aliases: oh]
  obs-all   Show all obs [aliases: oa]
  var-head  Show first n var [aliases: vh]
  var-all   Show all var [aliases: va]
  shape     Show shapes of obs and var [aliases: s]
  field     Show fields in obs and var [aliases: f]
  help      Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help
  -V, --version  Print version

Example

❯ adview oh -n 5 path/to/adata.h5ad

batch   _index  gene_count      umi_count
126     AAACCCAAGACTTCGT        1       1
126     AAACCCAAGCCTTTGA        3       3
128     AAACCCAAGTATGAAC        1       1
128     AAACCCAAGTCCGTCG        1       1
128     AAACCCAAGTGCAACG        1       1

❯ adview vh -n 5 path/to/adata.h5ad

_index  feature_types   gene_symbols
ENSG00000243485 Gene Expression MIR1302-2HG
ENSG00000237613 Gene Expression FAM138A
ENSG00000186092 Gene Expression OR4F5
ENSG00000238009 Gene Expression AL627309.1
ENSG00000239945 Gene Expression AL627309.3

❯ adview s path/to/adata.h5ad

obs shape: 15235
var shape: 36601

❯ adview f path/to/adata.h5ad

obs fields:
        batch (categorical)
        _index (string-array)
        gene_count (array)
        umi_count (array)

var fields:
        _index (string-array)
        feature_types (categorical)
        gene_symbols (categorical)

Contribution

code: wenjiewei

inspiration: liyang,lounan,wenhao,dingyi

License

MIT