Hello Friend!
This is a script designed to make comparisons between multiple genomes and specific databases (CARD, BacMet and VFDB). If you have another database in mind, feel free to send a request to dlnrodrigues@ufmg.br and we will update the code. The figure created by the script is known as a clustermap and by default uses a Euclidean distance measure to group the data.
IMPORTANT INFORMATION: The PanViTa tool is free to use under registration 20210006 of the Federal University of Minas Gerais, and is therefore the intellectual property of the institution. For this reason unofficial changes to the original script will not be allowed without prior consent.
To use the script it is possible to use the command:
python3 panvita.py
or
python3 panvita.py -h
Basically it is possible to use this tool through the command:
python3 panvita.py -card -vfdb -bacmet *.gbk
IMPORTANT INFORMATION: As input you must use .gbk, .gbf or .gbff files.
User, you will be able to obtain this script using the simple command:
git clone https://github.com/dlnrodrigues/panvita.git
cd panvita
python3 panvita.py -u
python3 panvita.py -h
Yes, we use dependencies to make this tool work. Therefore it will try to obtain all dependencies and databases automatically, however, if it is not possible you will have to obtain them by traditional means.
pip install wget
pip install seaborn
pip install pandas
pip install matplotlib
pip install basemap
If you have conda support, the following commands may work:
conda install -c anaconda wget
conda install seaborn
conda install pandas
conda install -c conda-forge matplotlib
conda install -c anaconda basemap
PanViTa uses some parameters to work properly. They are listed bellow.
-bacmet Antibacterial Biocide and Metal Resistance Genes Database
-card Comprehensive Antibiotic Resistance Database
-vfdb Virulence Factor Database
-update Update databases and dependences
-u Same as -update
-help Print this help
-h Same as -help
-v Print version and exit
-keep Maintains the protein sequences used, as well as the CDS position files
-k Same as -keep
-i Minimum identity to infer presence (default = 70)
-c Minimum coverage to infer presence (default = 70)
-d Force to use DIAMOND from system
-pdf Figures will be saved as PDF (default)
-png Figures will be saved as PNG (WARNING! High memory consumption)
-g Download the genomes fasta files (require CSV table from NCBI)
-a Download and annote the genomes using PROKKA pipeline (require CSV table from NCBI)
-b Download the genome GenBank files (require CSV table from NCBI)
-s Keep the locus_tag as same as the strain (require -b)
-m Get the metadata from BioSample IDs (require CSV table from NCBI)
If you have found our tool useful, please don't forget to quote us in your publications.
Rodrigues, D. L. N. et al. PanViTa: Pan Virulence and resisTance analysis. Frontiers in Bioinformatics 3, (2023).