Cell Type Annotation Tools

This repository provides schema of the cell type annotation and related data standardization operations.

Installation

Install the latest pypi package through following the instructions in the pypi page.

Configuration Spec

Configuration spec defines schema for the CTA data conversion config files. Latest schema is located at: ctat_schema.yaml

Operations

Cell Type Annotation Tool provides the following operations:

Validate

The provided YAML/YML configuration file is validated against the Cell Type Annotation Schema.

ctat validate -i /path/to/my_config.yaml

If config is valid, program exits with system code 0, otherwise logs the issues and exits with a non-zero code.

Format

Formats the given data into standard cell type annotation data structure using the given configuration. Output is persisted as a json file.

ctat format -i /path/to/my_data.tsv -c /path/to/my_config.yaml -o /path/to/output.json

Fields that are not mapped in the config file are stored as userAnnotations.

A sample configuration file can be found at test_config.yaml. After applying this config to the user data, sample output file can be found at test_result.json.