cap-validator

Overview

Python tool for validating H5AD AnnData files before uploading to the Cell Annotation Platform. The same validation code is used in Cell Annotation Platform following requirements from the CAP-AnnData schema published here.

Features

• ✨ Validates all upload requirements and returns results at once
• 🚀 RAM efficient
• 🧬 Provides a full list of supported ENSEMBL gene IDs for Homo sapiens and Mus musculus

Installation

pip install -U cap-upload-validator

Usage

Basic usage

from cap_upload_validator import UploadValidator

h5ad_path = "path_to.h5ad"

uv = UploadValidator(h5ad_path)
uv.validate()

Full documentation could be found in GitHub Wiki

CLI interface

$ capval tmp/tmp.h5ad
CapMultiException: 
AnnDataMissingEmbeddings: 
        The embedding is missing or is incorrectly named: embeddings must be a [n_cells x 2] 
        numpy array saved with the prefix X_, for example: X_tsne, X_pca or X_umap.
        
AnnDataMisingObsColumns: 
            Required obs column(s) missing: file must contain 
            'assay', 'disease', 'organism' and 'tissue' fields with valid values.
        
For details visit: 
        https://github.com/cellannotation/cap-validator/wiki/Validation-Errors

$ capval --help
usage: capval [-h] adata_path

CLI tool to validate an AnnData H5AD file before uploading to the Cell Annotation Platform.
The validator will raise CAP-specific errors if the file does not follow the CAP AnnData Schema,
as defined in:
https://github.com/cellannotation/cell-annotation-schema/blob/main/docs/cap_anndata_schema.md

Full documentation, including a list of possible validation errors, is available at:
https://github.com/cellannotation/cap-validator/wiki

Usage Example:
    `capval path/to/anndata.h5ad`

positional arguments:
  adata_path  Path to the AnnData h5ad file.

optional arguments:
  -h, --help  show this help message and exit

License

BSD 3-Clause License