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Upload Visualisation

Supports .json format only

How to Create the Visualisation

Prerequisites

This instructions work for Linux and MacOS. If you are working on Windows Windows Subsystem for Linux (WSL) is recommanded.

To create the visualisation, follow these steps:

  1. Install Miniconda

    Download and install Miniconda for your operating system.

  2. Download Required Tools
    • Download and extract the folder Astral Pro 3 from GitHub.
    • Download and extract the folder Scripts.zip file and extract the folder.

Installation Commands

For Debian (Ubuntu) and MacOS with Intel chip:

conda create --name PanBGC_vis -c conda-forge -c bioconda zol

For MacOS with Apple Silicon chip:

CONDA_SUBDIR=osx-64 conda create -n PanBGC_vis -c conda-forge -c bioconda zol

The rest is the same for all operating systems:

conda activate PanBGC_vis
pip install openpyxl tqdm

Note: If you want to use all the annotation libraries, you can remove the -m flag from the following command. This will increase download an run time.

setup_annotation_dbs.py -m

Running the Pipeline

After installing the prerequisites and setting up your environment, follow these steps to run the pipeline:

  1. Extract the Scripts

    Extract the downloaded Scripts.zip file to a location of your choice.

  2. Navigate to the Scripts Directory
    cd /path/to/extracted/Scripts
  3. Run the Pipeline

    Note: If visualising a single Gene Cluster Family (GCF), the input folder can contain the GenBank files directly. If visualising multiple GCFs, select a folder that contains subfolders, each representing a GCF with its respective GenBank files. No other changes are required.

    Execute the PanBGC.py script with the following parameters:

    python PanBGC.py -i /path/to/input_folder -o /path/to/result_folder -log /path/to/result_folder/log -c number_of_threads -al /path/to/astral-pro3

    Note: The astral-pro3 executable can be found in the downloaded and unzipped Astral-Pro3 folder under ASTER-Linux/bin/astral-pro3

  4. Parameters Explained
    • -i: Path to the input folder containing your GenBank files
    • -o: Path to the output folder where results will be saved
    • -log: Path for the log file
    • -c: Number of CPU threads to use
    • -al: Path to the astral-pro3 executable
  5. Upload Results

    Once the pipeline completes, the output will include a Visualisation.json file that you can upload using the form on the left.

Important: After running the pipeline, the Visualisation.json file will be located at:

/path/to/result_folder/signal_family/Final_Results/Visualisation.json

Example Command

python PanBGC.py -i ~/data/genomes -o ~/results/analysis -log ~/results/analysis/pipeline.log -c 4 -al ~/tools/ASTER-Linux/bin/astral-pro3