FATHOM(1)

✨ NAME ✨

okay so bestie, welcome to FATHOM(1) from the User Commands section 💖 this is the manual for fathom — the sequence and annotation tool. so the NAME vibe is literally: fathom - sequence and annotation tool 🌸

🌈 SYNOPSIS 🌈

the shape of this command is:

fathom <ann> <dna> <commands>

so you run fathom, then give it <ann>, <dna>, and <commands>. that's the whole synopsis, periodt 💅

🎀 OPTIONS 🎀

no cap, here's every single option, and I'm not skipping a crumb:

• -help — report useful information. it's giving helpful bestie energy, fr fr.
• -validate [-quiet] — this one has an optional -quiet bestie tagging along.
• -gene-stats [-errors-ok -nucleotide -dinucleotide] — optional squad inside the brackets: -errors-ok, -nucleotide, -dinucleotide.
• -categorize <int> — it wants an <int>, and that's the tea.
• -export <int> [-plus -errors-ok] — takes an <int>, with optional -plus and -errors-ok in the bracket.
• -extract <feature> -length <int> -offset <int> — needs <feature>, plus -length <int> and -offset <int>. iconic trio.
• -exon-intron — solo command, no extra args, main character energy.
• -split <-number <int> | -training <float> | -GC <float> | -repeat <float>> — pick one from this little menu: -number <int> or -training <float> or -GC <float> or -repeat <float>. the | means "or", bestie.
• -ace-format <-gene-method <string> [-dna -extra <string>]> — needs -gene-method <string>, and inside that you can optionally add -dna and -extra <string>.
• -compare-genes <predictions> [-details] — takes <predictions>, and -details is optional if you want that extra garnish.
• -score-genes <hmm> [-errors-ok] — takes <hmm>, with optional -errors-ok in the bracket.
• -filter-genes <hmm> -min-score <float> -min-length <int> — needs <hmm>, then -min-score <float> and -min-length <int>. she's demanding but valid.

lowkey, the original page doesn't spill more lore than this for the options, so I'm keeping it exactly as it is. no invented behavior, no extra claims, just the syntax and the one -help description. 🫶

mwah 💋 this page is fathom 2010-07-28, dated October 2013, from section FATHOM(1). bye bestie, slay responsibly ✨