GT-INLINESEQ_ADD(1)

📦
version 1.6.6 · 5 versions
, in ubuntu resolute, ubuntu stonking

💖 GT-INLINESEQ_ADD 💖

okay bestie, so you know how your GFF3 file is out here being all "i have features ✨" but with absolutely zero actual sequence letters to back it up?? tragic. this little icon of a tool — gt-inlineseq_add, part of the GenomeTools Manual (section 1, she's fancy) — rolls up with sequences from somewhere else and adds them inline to your GFF3 input. it's giving glow-up. it's giving main character energy. 🦋

🌸 SYNOPSIS 🌸

gt inlineseq_add [options] [GFF3_file ...]

like. that's it. that's the whole vibe. options optional, GFF3 files optional-ish, chaos welcome. 💅

✨ DESCRIPTION ✨

so here's the tea, and also every single flag, because I would never gatekeep:

  • -seqfile [filename] — points at the sequence file we're stealing sequences from. default: undefined (she's mysterious, she's nothing, she's undefined).
  • -encseq [filename] — instead of a plain sequence file, you can hand her an encoded sequence indexname to pull sequences from. default: undefined too. bestie is empty-handed until you say otherwise.
  • -seqfiles — this one sets the sequence files from which to extract the features. heads up: use -- to terminate the list of sequence files, otherwise she'll keep eating arguments like it's an unlimited pasta bar. 🍝
  • -matchdesc [yes|no] — search the sequence descriptions from the input files for the desired sequence IDs (the ones in your GFF3), and report the first match she finds. default: no.
  • -matchdescstart [yes|no] — same idea but stricter, queen: exactly match the sequence descriptions from the input files against the desired sequence IDs (in GFF3), matching from the beginning all the way to the first whitespace. no fuzzy nonsense. default: no.
  • -usedesc [yes|no] — use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries. and if a description contains a sequence range — for example III:1000001..2000000 — then the first part becomes the sequence ID (III) and the first range position becomes the offset (1000001). default: no.
  • -regionmapping [string] — set the file containing the sequence-region to sequence file mapping. default: undefined. very "bring your own map" of her.
  • -o [filename] — redirect output to the specified file. default: undefined, which honestly just means she'll yell into the terminal like a normal Tuesday.
  • -gzip [yes|no] — write a gzip compressed output file. default: no.
  • -bzip2 [yes|no] — write a bzip2 compressed output file. default: no.
  • -force [yes|no] — force writing to the output file. default: no. (she's polite until you tell her not to be 💀)
  • -help — display help and exit. she'll explain herself. iconic.
  • -version — display version information and exit. 🎀
ngl, that -usedesc range thing is the part everyone forgets, so like. read it twice. the offsets will get you. 😭

🙈 REPORTING BUGS 🙈

found a bug?? first of all, not me manifesting that. second of all, report it here:

https://github.com/genometools/genometools/issues

and that's the whole page bestie!! this was <b>GenomeTools 1.6.6</b>, dated <b>11/09/2025</b>, from the GenomeTools Manual, section 1 — GT-INLINESEQ_ADD(1) — and she ate, no crumbs. go add some sequences. slay. 👑💜

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