This python script generates an interactive summary report from fusion detection tools. Fusion-report is part of a bigger project nf-core/rnafusion which is designed to detect and report fusion genes from RNA-seq data.
TL;DR: Live demo here.
Supported tools
Installation
Using Conda
conda install -c bioconda fusion-report=2.1.4From source
sudo apt-get install sqlite3
python3 setup.py installUsage
# Download required databases
# Currently supported databases: FusionGDB, Mitelman and COSMIC
# COSMIC requires login credentials to download Fusion gene Database
fusion_report download --cosmic_usr '<username>' --cosmic_passwd '<password>' /path/to/db/
# Run the fusion-report
fusion_report run "<SAMPLE NAME>" /path/to/output /path/to/db/ \
--arriba tests/test_data/arriba.tsv \
--dragen tests/test_data/dragen.tsv \
--ericscript tests/test_data/ericscript.tsv \
--fusioncatcher tests/test_data/fusioncatcher.txt \
--pizzly tests/test_data/pizzly.tsv \
--squid tests/test_data/squid.txt \
--starfusion tests/test_data/starfusion.tsv \
--jaffa tests/test_data/jaffa.csv \
--allow-multiple-gene-symbols # in case gene symbol in fusion can't be determined, treat each provided fusion as a separate one.Or get help and list all possible parameters.
fusion_report --help
fusion_report run --help
fusion_report download --help
fusion_report sync --helpFor more info on how to run the script, please see the documentation.
Credits
- Testing dataset copied from ndaniel/fusioncatcher.
- DNA icon made by Freepik from Flaticon is licensed by CC 3.0 BY.