SingleCellSchema

The SingleCellSchema repository houses developments related to Earlham Institute's (EI’s) CELLGEN ISP metadata mapping and schemas, designed to describe a variety of Single Cell Genomics and Spatial Transcriptomics experiment types, such as those from 10X Genomics and Vizgen.

It contains the following directories:

• dist: contains the output files generated from the conversion process.

• schemas: contains the core, extended and general versions of the schema in JSON format.

• utils: contains Python helper scripts to convert JSON files into tabular formats such as Excel.

The main script, convert.py, is used to convert the JSON schema into Excel, XML, and additional JSON files. It is found in the project root directory.

Abbreviations:

• SC RNASEQ: Single Cell RNA-Sequencing
• STX: 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

   Core directories

   mkdir dist/checklists/core/json

   mkdir dist/checklists/core/xml

   mkdir dist/checklists/core/xlsx

   Extended directories

   mkdir dist/checklists/extended/json

   mkdir dist/checklists/extended/xml

   mkdir dist/checklists/extended/xlsx

6. Different ways to run the convert.py script which is found in the project root directory

   • Use launch.json file to run the script in VSCode by selecting the appropriate configuration

     --OR--

   • python3 convert.py

     This will convert the schema into an excel file, xml and json files using all termsets, standards and schemas in the schemas/base directory

     --OR--

   • python3 convert.py <termset>

     where <termset> is the type of terms to be used (extended, core) e.g. python3 convert.py core

     --OR--

   • python3 convert.py schemas/base/<schema-name> <termset>

     where <schema-name> is the name of the schema file in the schemas directory, <termset> is the type of terms to be used (extended, core) e.g. python3 convert.py schemas/base/sc_rnaseq.json core

     --OR--

   • python3 convert.py schemas/base/<schema-name> <termset> <standard>

     where <schema-name> is the name of the schema file in the schemas directory, <termset> is the type of terms to be used (extended, core) and <standard> is the standard to be used (e.g. dwc, mixs, schemaorg) e.g. python3 convert.py schemas/base/sc_rnaseq.json core dwc

     --OR--

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

     python -m unittest