Panel Assigner v2

This tool is designed to take an R code and return a list of genes and bed files for the requested test. A database storing the panel request information, the gene informations, and the bedfile can be created by pushing the information produced by running the tool to the database.

APP usage

Documentation on the installation and setup of the app can be found here.

Required Inputs: 1) Test directory code: -ID followed by test code ("RXXX")

python3 src/tool_v2.py -ID <"RXXX">

This will start the tool which performs the following:

• Checking the most recent version of the NGTD is being used, and updating if required
• Check that R code is in the NGTD, and check if the user wants to continue if not
• Query PanelApp with the requested R code, retrun warnings if the R code does not correspond to a NGS panel
• From the PanelApp query, extract the HGNC IDs for genes in the requested panel
• Use the HGNC IDs to query Variant Validator, and create a bedfile and json file for each gene in the requested panel
• Logging of commands and requests throughout

The output bed files will be stored in an output folder in a folder corresponding to the date and time the tool was run.

The information produced by the tool can be pushed to a database for later retrieval and interaction. Details on how to interact with the database can be found here.

An earlier version of the tool is available in a webpage format as well. Details on running the interactive webpage can be found here.

The tool can also be run using Docker. Details on using the docker can be found here.

Folder structure

Overview of existing folder structure

.
├── config
├── docs
├── frontend
│   ├── frontend
│   │   └── __pycache__
│   └── userinterface
│       ├── config
│       ├── migrations
│       │   └── __pycache__
│       ├── __pycache__
│       ├── static
│       │   └── userinterface
│       ├── templates
│       │   └── userinterface
│       └── ToolModule
│           └── __pycache__
├── images
├── output
│   ├── 25012024_101359
│   └── logs
├── src
│   └── database
├── test_directory_file
└── tests
    ├── bedfiles
    ├── gene_info_jsons
    ├── panel_info_jsons
    └── __pycache__

Testing

Testing is still in development. Tests currently exist for the functions get_hgncIDs and call_transcript_make_bed. These can be run with pytest from the root directory

Logging

Logging is performed throught the process of running the tool. The log is stored in `output/logs/runlog.log``

Plans for future development

Plans for future development are documented here.

Any current plans for future development are recorded in git issues.The desired end product is a tool to manage gene panels for NHS National genomic test directory tests in the laboratory and use this to record the testing carried out for individual patients.

Needing help

Need help running the tool? Details of how to request help can be found here.

Contributing

Alternatively if you would like to contribute to the project, details on how to do this can be found here