VIRULENCEFINDER.PY(1)

💖 VIRULENCEFINDER.PY 💖

okay bestie, so virulencefinder.py is the tool that helps you identify virulence genes in total or partial sequenced isolates of bacteria. that's the whole vibe. it's from the virulencefinder.py manual, section 1 (user commands), and honestly? iconic. 👑

✨ DESCRIPTION ✨

here's how you call her:

virulencefinder.py [-h] -i INFILE [INFILE ...] [-o OUTDIR]

[-tmp TMP_DIR] [-mp METHOD_PATH] [-p DB_PATH]
       [-d DATABASES] [-l MIN_COV] [-t THRESHOLD] [-x]
       [--speciesinfo_json SPECIESINFO_JSON] [-q]

(yeah the synopsis is a little chaotic, she's doing her best, we love her for it 🫶)

🎀 optional arguments 🎀

• -h, --help — shows this help message and dips. classic. ✨
• -i INFILE [INFILE ...], --infile INFILE [INFILE ...] — your FASTA or FASTQ input files. this is the the main character argument, literally required, no skipping. 💅
• -o OUTDIR, --outputPath OUTDIR — path to the blast output. tell her where to put the goods. 🍓
• -tmp TMP_DIR, --tmp_dir TMP_DIR — temporary directory for storage of the results from the external software. just a lil holding pen, nbd. 🧚
• -mp METHOD_PATH, --methodPath METHOD_PATH — path to the method you wanna use, either kma or blastn. pick your fighter. 🔥
• -p DB_PATH, --databasePath DB_PATH — path to the databases. show her where the data lives. 💜
• -d DATABASES, --databases DATABASES — databases chosen to search in. if none is specified, all of them get used. go big or go home, no cap. 👑
• -l MIN_COV, --mincov MIN_COV — minimum coverage. set your bar, bestie. ⭐
• -t THRESHOLD, --threshold THRESHOLD — minimum threshold for identity. (the original says "hreshold" and honestly? we're keeping that energy, typos are valid 😭)
• -x, --extented_output — gives extented output with alignment files, template and query hits in fasta, plus a tab separated file with gene profile results. so much output, we're obsessed. 🌈
• --speciesinfo_json SPECIESINFO_JSON — an argument used by the cge pipeline. it takes a list in json format consisting of taxonomy, from domain → species. a database gets chosen based on the taxonomy. fancy. 💖
• -q, --quiet — quiet mode. no notes, no commentary, just vibes. 🤫

🌸 AUTHOR 🌸

this manpage was written by Nilesh Patra for the Debian distribution, and can be used for any other usage of the program. king behavior fr fr. 👑

and that's the whole page bestie!! 💖 this is virulencefinder.py version 2.0.4, dated July 2021, straight from the VIRULENCEFINDER.PY(1) source. now go find those virulence genes, you absolute legend. ✨🦋💅