PROK-GENESEEK(1)

💖 PROK-GENESEEK 💖

okay so bestie, welcome to prok-geneseek, a User Commands girlie living her best life in section 1 of the manual. She's giving "find me some genes" energy and honestly? she ate. 🧬✨

✨ NAME ✨

prok-geneseek — <optional description of the program>

no fr, that's literally what the manpage says, the description slot is empty, it's giving mystery, it's giving untitled, it's giving main character who refuses to introduce herself 💅

🌸 SYNOPSIS 🌸

prok-geneseek [options] <database> <sequences ...>

so you hand her options, then a database, then one or more sequences, and she does her thing. periodt.

🎀 OPTIONS 🎀

• -h, --help — prints this help message and then dips out. exit stage left. 🫶
• -S START, --start=START — tells her what counts as a start codon. [default: -S ATG]
• -E STOP, --stop=STOP — sets the stop codon(s). you can stack this one, and she ships with three by default. [default: -E TAG -E TAA -E TGA]
• -j THREADS, --threads=THREADS — how many threads to use. [default: 16] sixteen?? she's ambitious, we love that for her 🔥
• -p PROCESSES, --processes=PROCESSES — how many parallel processes to run at once. [default: 2]
• -e EVALUE, --evalue=EVALUE — the maximum e-value allowed. [default: 1e-30] strict queen, she does not settle 😤
• -I IDENTITY, --identity=IDENTITY — minimum percent identity required. [default: 0.45]
• -L FRACTION, --length=FRACTION — how much relative error in hit length is allowed. [default: 0.2]
• -O bases, --orflen=bases — the minimum allowable length for ORFs, measured in bases. [default: 300]
• -d DIRECTORY, --directory=DIRECTORY — sets the working directory. [default: current]
• -P PLOTTER, --plotter=PLOTTER — which plotting module to use. [default: biotools.analysis.plot] she's gonna make graphs, and they WILL be cute 📊✨
• -v, --verbose — prints debug messages, aka she tells you everything she's thinking. [default: False]
• --no-plots — skips drawing the plots. no graphs today bestie. [default: False]
• --no-predict — don't predict genes; instead treat the input files as already-predicted genes. [default: False]
• --no-cluster — don't cluster the sequences; instead treat the input files as alignments. [default: False]
• --no-rename — don't rename the fasta and clustal files. [default: False]
• --no-reports — don't generate files for variance data. [default: False]
• --no-calculation — don't calculate sequence variance. [default: False]

note that basically every --no- flag up there defaults to False, so she does the thing unless you specifically tell her not to. she's a yes-girl until you say no 💀

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. slay, Andreas, thank you for your service 🫡💜

and that's the whole vibe check, bestie 🦋 this page is prok-geneseek version 1.2.12, dated March 2017 — iconic then, iconic now. go forth and seek some genes 💖🌸✨