GT-CONVERTSEQ(1)

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

💖 GT-CONVERTSEQ — the GenomeTools manual, but make it cute ✨

okay bestie, welcome to the GT-CONVERTSEQ(1) page from the GenomeTools Manual 🌸 this is the little tool that parses and converts sequence file formats — FASTA/FASTQ, GenBank, EMBL — and honestly? she ate. let's get into it 🫶

✨ NAME ✨

gt-convertseq — parse and convert sequence file formats (FASTA/FASTQ, GenBank, EMBL). no cap, that's the whole job and she does it flawlessly 💅

🌈 SYNOPSIS 🌈

gt convertseq [options] file [...]

so you call her with gt convertseq, throw some options at her, and then hand her one or more files. she's not picky, she'll take a whole stack of them 📚✨

🦋 DESCRIPTION 🦋

okay so here's every single option, and I mean every one, because we do not gatekeep in this house 👑

  • -v [yes|no] — be verbose (default: no). she'll talk more if you let her 🗣️
  • -r [yes|no] — reverse complement sequences (default: no). flip it and reverse it 🔄
  • -showfilelengthvalues [yes|no] — show filelengths (default: no) 📏
  • -noseq [yes|no] — do not show sequences (default: no). yes the name is a little cursed but it literally means "no seq", as in, don't print the sequences 🙈
  • -fastawidth [value] — FASTA output line width, 0 for unlimited (default: 60) 📐
  • -contractdnawc [yes|no] — replace stretches of DNA wildcards with a single N (default: no) 🧬
  • -contractproteinwc [yes|no] — replace stretches of protein wildcards with a single X (default: no) 🧪
  • -o [filename] — redirect output to specified file (default: undefined) 📁
  • -gzip [yes|no] — write gzip compressed output file (default: no) 🗜️
  • -bzip2 [yes|no] — write bzip2 compressed output file (default: no) 🗜️
  • -force [yes|no] — force writing to output file (default: no) 💪
  • -help — display help and exit 🆘
  • -version — display version information and exit 🏷️
reminder bestie: the [yes|no] ones all default to no, and -fastawidth defaults to 60, and -o has no default at all (it's just undefined until you give her a filename). don't come for me, that's just what the page says 💀

😭 REPORTING BUGS 😭

found a bug? don't suffer in silence, tell the devs fr fr:

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

and that's the whole page, you're officially a gt-convertseq girlie now 🎀

GenomeTools 1.6.6 🌟 11/09/2025 — mwah, that's the version and date, go forth and convert those sequences, periodt 💅✨🦋

📦 where this page comes from