AVERAGE_NUCLE...E_IDENTITY.PY(1)

✨ NAME ✨

average_nucleotide_identity.py — average nucleotide identity 💖

🦋 DESCRIPTION 🦋

okay so bestie, here's the whole vibe of this script — it's giving "average nucleotide identity" and honestly it's so much. here's how you're supposed to call it:

average_nucleotide_identity.py [-h] [--version] -o OUTDIRNAME -i INDIRNAME [-v] [-f] [-s FRAGSIZE] [-l LOGFILE] [--skip_nucmer] [--skip_blastn] [--noclobber] [--nocompress] [-g] [--gformat GFORMAT] [--gmethod {mpl,seaborn}] [--labels LABELS] [--classes CLASSES] [-m {ANIm,ANIb,ANIblastall,TETRA}] [--scheduler {multiprocessing,SGE}] [--workers WORKERS] [--SGEgroupsize SGEGROUPSIZE] [--SGEargs SGEARGS] [--maxmatch] [--nucmer_exe NUCMER_EXE] [--filter_exe FILTER_EXE] [--blastn_exe BLASTN_EXE] [--makeblastdb_exe MAKEBLASTDB_EXE] [--blastall_exe BLASTALL_EXE] [--formatdb_exe FORMATDB_EXE] [--write_excel] [--rerender] [--subsample SUBSAMPLE] [--seed SEED] [--jobprefix JOBPREFIX]

🎀 optional arguments 🎀

these are the levers you can pull, and no cap there are a lot of them:

• -h, --help — pops this help message and dips 💅
• --version — shows the program's version number and exits, periodt
• -o OUTDIRNAME, --outdir OUTDIRNAME — where the output directory lives. required, so don't forget it bestie 😭
• -i INDIRNAME, --indir INDIRNAME — the input directory name. also required fr fr
• -v, --verbose — give verbose output, so it tells you everything it's doing 🗣️
• -f, --force — force file overwriting. bold. slay. but careful 👀
• -s FRAGSIZE, --fragsize FRAGSIZE — sequence fragment size for ANIb (default 1020)
• -l LOGFILE, --logfile LOGFILE — logfile location 📝
• --skip_nucmer — skip NUCmer runs, for testing (e.g. if output already present)
• --skip_blastn — skip BLASTN runs, for testing (e.g. if output already present)
• --noclobber — don't nuke existing files 🫶 (very demure of you)
• --nocompress — don't compress/delete the comparison output
• -g, --graphics — generate heatmap of ANI 🔥
• --gformat GFORMAT — graphics output format(s) [pdf|png|jpg|svg] (default pdf,png,eps meaning three file formats)
• --gmethod {mpl,seaborn} — graphics output method (default mpl)
• --labels LABELS — path to file containing sequence labels 🏷️
• --classes CLASSES — path to file containing sequence classes
• -m {ANIm,ANIb,ANIblastall,TETRA}, --method {ANIm,ANIb,ANIblastall,TETRA} — ANI method (default ANIm) ✨
• --scheduler {multiprocessing,SGE} — job scheduler (default multiprocessing, i.e. locally)
• --workers WORKERS — number of worker processes for multiprocessing (default zero, meaning use all available cores) 💪
• --SGEgroupsize SGEGROUPSIZE — number of jobs to place in an SGE array group (default 10000)
• --SGEargs SGEARGS — additional arguments for qsub
• --maxmatch — override MUMmer to allow all NUCmer matches
• --nucmer_exe NUCMER_EXE — path to NUCmer executable
• --filter_exe FILTER_EXE — path to delta-filter executable
• --blastn_exe BLASTN_EXE — path to BLASTN+ executable
• --makeblastdb_exe MAKEBLASTDB_EXE — path to BLAST+ makeblastdb executable
• --blastall_exe BLASTALL_EXE — path to BLASTALL executable
• --formatdb_exe FORMATDB_EXE — path to BLAST formatdb executable
• --write_excel — write Excel format output tables 📊
• --rerender — rerender graphics output without recalculation (no redo of the math, just the glow-up 💅)
• --subsample SUBSAMPLE — subsample a percentage [0-1] or specific number (1-n) of input sequences
• --seed SEED — set random seed for reproducible subsampling.
• --jobprefix JOBPREFIX — prefix for SGE jobs (default ANI).

👑 AUTHOR 👑

this manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. iconic behavior, honestly 🙌

ok bestie that's the whole page, go forth and compute those identities 🧬✨ — this was average_nucleotide_identity.py, July 2021, mwah 💖🦋🎀