This repository contains developments regarding EI's CELLGEN ISP metadata standards.

Broadly, the schemas can be used for describing a range of single cell genomic and spatial transcriptomics experiment types such as 10X and Vizgen. The schemas directory contains the JSON representation of the schema, and the utils directory contains python modules to convert from json to tabular formats such as excel.

Abbreviations:

• SC RNASEQ: Single Cell RNA-Sequencing
• SPAT: Spatial Transcriptomics

Please follow the instructions below to convert the JSON schema to an excel file, xml and json files:

1. Download or clone this repository and navigate to its directory in the terminal

   git clone https://github.com/TGAC/SingleCellSchemas.git

   cd SingleCellSchemas

2. Create a new Python virtual environment called venv

   python3 -m venv venv

3. Activate the virtual environment

   source venv/bin/activate

4. Install dependencies

   pip3 install -r requirements/requirements.txt

5. Make the following directories if they do not exist

   mkdir dist/checklists/json

   mkdir dist/checklists/xml

   mkdir dist/checklists/xlsx

6. Run the converter script

   Use launch.json file to run the script in VSCode

   --OR--

   python convert.py schemas/<data-type> dist/checklists/<output-format>/<output-name>.xlsx

   where <data-type> is the name of the schema file in the schemas directory, <output-format> is the format of the output file (json, xml, xlsx) and <output-name> is the name of the output file.

   --OR--

   Run the tests (which also runs the converter whilst verifying the output)

   python -m unittest