GT-CHSEQIDS(1)

💖 GT-CHSEQIDS(1) 💖

the GenomeTools manual, but make it a group chat ✨

okay so bestie, welcome to gt-chseqids — part of the GenomeTools crew 🧬💅

---

🌸 NAME 🌸

gt-chseqids — change sequence ids by the mapping given in a mapping file. that's it, that's the whole job, and it does it flawlessly 👑

---

✨ SYNOPSIS ✨

gt chseqids [option ...] mapping_file [GFF3_file]

so it's gt chseqids, then some options if you're feeling fancy, then your mapping_file (required, no skipping), then optionally a GFF3_file 🦋

---

🎀 DESCRIPTION 🎀

bestie here's the whole option menu, and yes we're going through every single one because you deserve the full tea ☕

• -sort [yes|no] — sort the GFF3 features after changing the sequence ids. heads up: memory consumption is proportional to the input file size 📈 (default: no)
• -v [yes|no] — be verbose. like, tell me everything (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 ✨

---

🦋 File format for mapping_file 🦋

so the mapping file you hand over defines a mapping table named chseqids. what does it do? it maps the sequence-region entries given in the GFF3_file to other names. main character behavior tbh 💅

you can define it like this:

chseqids = {
  chr1  = "seq1",
  chr2  = "seq2"
}

when this example is used, all sequence ids chr1 will be changed to seq1 and all sequence ids chr2 to seq2. iconic. no notes. periodt 💖

---

😭 REPORTING BUGS 😭

found a bug? report bugs to https://github.com/genometools/genometools/issues. they'll handle it, we don't gatekeep 🫶

---

and that's the whole page bestie!! 🌈 this was GenomeTools 1.6.6, dated 11/09/2025, and honestly? she ate. go change those sequence ids, you absolute legend 👑💜🌸