RUN_RESFINDER.PY(1)

💖 RUN_RESFINDER.PY(1) 💖

okay so you found your way into the User Commands corner of the manual and the thing you're looking at is run_resfinder.py 🦋 — the script that sniffs out acquired antimicrobial resistance genes. sit down, grab a strawberry, and let's get into it bestie, because this one has a lot of flags and every single one of them matters 💅

✨ NAME ✨

run_resfinder.py — identify acquired antimicrobial resistance genes 🔥

🌸 DESCRIPTION 🌸

the way this program wants to be called is literally this, no cap:

usage: run_resfinder.py [-h] [-ifa INPUTFASTA]
       [-ifq INPUTFASTQ [INPUTFASTQ ...]] [-o OUT_PATH]
              [-b BLAST_PATH] [-k KMA_PATH] [-s SPECIES] [-db_res DB_PATH_RES]
              [-db_res_kma DB_PATH_RES_KMA] [-d DATABASES] [-acq] [-ao
              ACQ_OVERLAP] [-l MIN_COV] [-t THRESHOLD] [-c] [-db_point
              DB_PATH_POINT] [-db_point_kma DB_PATH_POINT_KMA] [-g
              SPECIFIC_GENE [SPECIFIC_GENE ...]] [-u] [-l_p MIN_COV_POINT]
              [-t_p THRESHOLD_POINT] [--pickle]

that's the whole vibe check right there. now let's break down every single argument, because we are not skipping any of them 👑

🎀 optional arguments 🎀

• -h, --help — shows this help message and exits. the classic. the icon. when in doubt, ask for help, periodt 💖
• -ifa INPUTFASTA, --inputfasta INPUTFASTA — your input fasta file. just the one. singular. she's a fasta girly 🧚
• -ifq INPUTFASTQ [INPUTFASTQ ...], --inputfastq INPUTFASTQ [INPUTFASTQ ...] — input fastq file(s). and here's the tea: if you hand over only one file it's assumed to be single-end fastq, and if you hand over two files it's assumed to be paired-end data. two files = couple goals fr fr 💞
• -o OUT_PATH, --outputPath OUT_PATH — path to blast output. where the receipts go 📝
• -b BLAST_PATH, --blastPath BLAST_PATH — path to blastn. point her at the binary bestie 🔍
• -k KMA_PATH, --kmaPath KMA_PATH — path to KMA. yes, that KMA. the kmer bestie 🫶
• -s SPECIES, --species SPECIES — species in the sample. like, who are we even talking about here 🌈
• -db_res DB_PATH_RES, --db_path_res DB_PATH_RES — path to the databases for ResFinder 🗂️
• -db_res_kma DB_PATH_RES_KMA, --db_path_res_kma DB_PATH_RES_KMA — path to the ResFinder databases indexed with KMA. defaults to the 'kma_indexing' directory inside the given database directory. lowkey convenient ✨
• -d DATABASES, --databases DATABASES — the databases you've chosen to search in. and if none is specified, all of them get used. go big or go home 💅
• -acq, --acquired — runs resfinder for acquired resistance genes. that's the whole point of her 🎯
• -ao ACQ_OVERLAP, --acq_overlap ACQ_OVERLAP — genes are allowed to overlap this number of nucleotides. default: 30. let them overlap a little, it's fine 😌
• -l MIN_COV, --min_cov MIN_COV — minimum (breadth-of) coverage of ResFinder. set the bar, bestie 📏
• -t THRESHOLD, --threshold THRESHOLD — threshold for identity of ResFinder. how close is close enough 👀
• -c, --point — runs pointfinder for chromosomal mutations. different beast, same energy 🧬
• -db_point DB_PATH_POINT, --db_path_point DB_PATH_POINT — path to the databases for PointFinder 🗃️
• -db_point_kma DB_PATH_POINT_KMA, --db_path_point_kma DB_PATH_POINT_KMA — path to the PointFinder databases indexed with KMA. defaults to the 'kma_indexing' directory inside the given database directory. twins with the ResFinder one, obsessed 💜
• -g SPECIFIC_GENE [SPECIFIC_GENE ...] — specify genes existing in the database to search for. if none is specified, all genes are included in the search. cherry-picking is allowed, slay 🍓
• -u, --unknown_mut — show all mutations found even if unknown to the resistance database. spill everything, even the mystery ones 😭
• -l_p MIN_COV_POINT, --min_cov_point MIN_COV_POINT — minimum (breadth-of) coverage of Pointfinder. if None is selected, the minimum coverage of ResFinder will be used. she borrows from her sister 🫶
• -t_p THRESHOLD_POINT, --threshold_point THRESHOLD_POINT — threshold for identity of Pointfinder. if None is selected, the minimum coverage of ResFinder will be used. yes, it says coverage, and we are quoting her exactly, no edits 💀
• --pickle — create a pickle dump of the Isolate object. currently needed in the CGE webserver. dependency and this option is being removed. so, like, don't build your whole life around it, it's on the way out 🙈

👑 AUTHOR 👑

this manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. absolute legend, we love a manpage author 💖

and that's the whole page bestie, no notes, you ate it 💅✨

run_resfinder.py 4.1.5 — July 2021 — that's the version and the date, tucked right at the end where the footer lives, mwah 🎀