GT-EXTRACTFEAT(1)

💖 GT-EXTRACTFEAT 💖

okay so bestie, welcome to gt-extractfeat from the GenomeTools Manual — yes the manual name goes here, slay, we move. This is the tool that goes and extracts the features you asked for out of your sequence files, based on the GFF3 file. it's giving little-miss-grabs-your-exons. 💅

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🌸 NAME 🌸

gt-extractfeat — pull the features listed in a GFF3 file out of a sequence file. that's it, that's the whole job, and she does it flawlessly ✨

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🦋 SYNOPSIS 🦋

gt extractfeat [option ...] [GFF3_file]

so it's the tool name, then whatever options you want, then optionally your GFF3 file. GFF3 file is optional, not me pointing that out or anything. 🙈

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🎀 DESCRIPTION 🎀

✨ the options, one by one, no skipping ✨

• -type [string] — tells her which type of features to extract. default: undefined (so like… say something, bestie).
• -join [yes|no] — joins the feature sequences that live in the same subgraph into one single sequence. default: no. they're getting fused, fr fr.
• -translate [yes|no] — translates the features (of a DNA sequence) into protein. default: no. glow-up from nucleotides to amino acids honestly.
• -seqid [yes|no] — adds the sequence ID of the extracted features to the FASTA descriptions. default: no.
• -target [yes|no] — adds the target ID(s) of the extracted features to the FASTA descriptions. default: no.
• -coords [yes|no] — adds the location of the extracted features to the FASTA descriptions. default: no.
• -retainids [yes|no] — uses the ID attributes of the extracted features as the FASTA descriptions. default: no. keeping the original names, iconic behaviour. 👑
• -gcode [value] — picks the genetic code to use. default: 1. (there's a whole list of these below, don't worry, she's thorough.)
• -seqfile [filename] — sets the sequence file to take the sequences from. default: undefined.
• -encseq [filename] — sets the encoded sequence indexname to take the sequences from. default: undefined.
• -seqfiles — sets the sequence files to extract the features from. use -- to terminate the list of sequence files. (yes, --, the little signal that the list is done. periodt.)
• -matchdesc [yes|no] — searches the sequence descriptions in the input files for the desired sequence IDs (in GFF3), and reports the first match. default: no.
• -matchdescstart [yes|no] — exactly matches the sequence descriptions from the input files for the desired sequence IDs (in GFF3) from the beginning all the way to the first whitespace. default: no.
• -usedesc [yes|no] — uses sequence descriptions to map the sequence IDs (in GFF3) to the actual sequence entries. if a description contains a sequence range (like, e.g., III:1000001..2000000), the first part gets used as the sequence ID (III) and the first range position gets used as the offset (1000001). default: no. the way she splits that up 😭
• -regionmapping [string] — sets the file containing the sequence-region to sequence file mapping. default: undefined.
• -v [yes|no] — be verbose. default: no. she will literally tell you everything.
• -width [value] — sets the output width for FASTA sequence printing (0 disables formatting). default: 0.
• -o [filename] — redirects output to the specified file. default: undefined.
• -gzip [yes|no] — writes a gzip compressed output file. default: no.
• -bzip2 [yes|no] — writes a bzip2 compressed output file. default: no.
• -force [yes|no] — forces writing to the output file. default: no. she's not asking permission, she's telling you. 💅
• -help — displays help and exits. our little "girl help" moment, but make it useful. 🫶
• -version — displays version information and exits.

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🧬 genetic code numbers for option -gcode 🧬

okay here's the whole roster, no cap, every single one:

1. Standard
2. Vertebrate Mitochondrial
3. Yeast Mitochondrial
4. Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
5. Invertebrate Mitochondrial
6. Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
9. Echinoderm Mitochondrial; Flatworm Mitochondrial
10. Euplotid Nuclear
11. Bacterial, Archaeal and Plant Plastid
12. Alternative Yeast Nuclear
13. Ascidian Mitochondrial
14. Alternative Flatworm Mitochondrial
15. Blepharisma Macronuclear
16. Chlorophycean Mitochondrial
21. Trematode Mitochondrial
22. Scenedesmus obliquus Mitochondrial
23. Thraustochytrium Mitochondrial
24. Pterobranchia Mitochondrial
25. Candidate Division SR1 and Gracilibacteria

bestie yes, the numbers skip. 7, 8, 17, 18, 19, 20 are just… not on the list. do not come for me, I'm only the messenger. 💀

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🌈 file format for option -regionmapping 🌈

the file you hand to -regionmapping defines a "mapping". a mapping maps the sequence-region entries given in the GFF3_file to a sequence file that contains the corresponding sequence. mappings can be defined in one of the following two forms:

mapping = {
  chr1  = "hs_ref_chr1.fa.gz",
  chr2  = "hs_ref_chr2.fa.gz"
}

or

function mapping(sequence_region)
  return "hs_ref_"..sequence_region..".fa.gz"
end

so, the tea: the first form defines a Lua (http://www.lua.org) table named "mapping" which maps each sequence region to the corresponding sequence file. the second one defines a Lua function "mapping", and that function has to return the sequence file name when it gets called with the sequence_region as its argument. two forms, one job, she ate. 🔥

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😭 REPORTING BUGS 😭

found a bug? report it, bestie, don't just suffer in silence:

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

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that's the whole page, you made it, I'm so proud 🥹💜 this was GenomeTools 1.6.6, dated 11/09/2025, and that's the cute little sign-off from yours truly. go extract something iconic. ✨👑💅