Metadata-Version: 2.1
Name: ctat
Version: 0.0.5.dev1
Summary: The aim of this project is to specify the Cell Type Annotation schema and related data standardization operations.
Home-page: https://github.com/hkir-dev/cell-type-annotation-tools
Author: 
License: Apache-2.0 license
Description: # Cell Type Annotation Tools
        
        This repository provides schema of the cell type annotation and related data standardization operations.
        
        ## Installation
        
        Install the latest [pypi package](https://pypi.org/project/ctat/) 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](src/schema/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](src/test/test_data/test_config.yaml). After applying this config to [the user data](src/test/test_data/AIT115_annotation_sheet.tsv), sample output file can be found at [test_result.json](src/test/test_data/test_result.json).
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
