RGA_VF_plot (script to visualize RGI and Abricate output files containing results of a search for ARGs of VFs)
Domain:
healthcareRecord type:
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■ ARG_VF_plot v1.1.2 ■
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📅 Created: 2025-10-21
👨💻 Author: Oleg Reva (oleg.reva@up.ac.za)
Centre for Bioinformatics and Computational Biology,
BGM, University of Pretoria, South Africa
🔬 Purpose:
Visualize output files of Abricate and RGI searches for virulence factors (VFs)
and antibiotic resistance genes (ARGs).
⚙️ Dependencies (minimum):
┌───────────────────┬───────────────────────┐
│ Tool │ Version │
├───────────────────┼───────────────────────┤
│ Python │ 3.12 │
│ json │ stdlib │
│ matplotlib │ 3.8+ │
│ pandas │ 2.2+ │
│ numpy │ 1.26+ │
└───────────────────┴───────────────────────┘
🚀 Usage:
python3 arg_vf_plot.py [options]
🔧 Options:
-I, --input-root • Input folder root (default: 'input')
-O, --output-root • Output folder root (default: 'output')
-i, --project • Project folder inside input root (default: 'S.enterica')
-j, --subproject • Sub-project inside project (default: '')
-t, --task • One of: Abricate, RGI (default: 'RGI')
-p, --plot • 'yes' or 'no' to show a plot (default: 'yes')
--menu • Open an interactive menu before running
-V, --version • Show version information
-h, --help • Show this help message
Notes:
• The script will create missing output directories as needed.
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Instead of command line argument setting, run:
py arg_vf_plot.py --menu
An interactive manu will be shown to set the arguments one by one:
Last update 2025/10/21
Settings for this run:
I Input folder root : input
i Project folder : (none)
j Project subfolder : (none)
O Output folder root : output
T Task : RGI
P Show plot : yes
Change [I/i/j/O/T/P], or press Y to accept, or Q to quit: