PANORAMA Test Datasets

Overview

This repository contains test datasets for PANORAMA project CI testing and validation.

Philosophy: "As small as possible, as large as necessary" - Test data are minimized but still functional for testing purposes.

Contents

• 3 Vibrio pangenomes from GTDB RefSeq PanGBank collection (in pangenomes/)
• 9 defense system models from Defense Finder (in models/)
• 34 HMM profiles from Defense Finder for model annotation (in hmms/)

Setup and Usage

Clone the Repository

git clone https://github.com/labgem/PANORAMA_test.git
cd PANORAMA_test

Getting Information on Input Pangenomes

panorama info -p pangenomes_list.tsv -o output --status --content 

Running System Detection

1. Format HMM profiles:

panorama utils --hmm hmms -o hmms_formatted/

2. Run annotation:

panorama annotation \
--pangenomes pangenomes_list.tsv \
--source defensefinder \
--hmm hmms_formatted/hmm_list.tsv \
--k_best_hit 3 \
--output results/

3. Prepare models and run systems detection:

panorama utils --models models/* -o .  --force
panorama systems \
--pangenomes pangenomes_list.tsv \
--models models_list.tsv \
--source defensefinder \
--annotation_sources  defensefinder 

4. Write systems results:

panorama write_systems  \
--pangenomes pangenomes_list.tsv \
--output write_systems_outdir \
--models models_list.tsv \
--sources defensefinder \
--projection \
--association all

License

This repository is licensed under the CECILL License.

Contact

For questions or suggestions regarding this dataset repository, please open an issue.