GT-CDS(1)

🎀 GT-CDS 🎀 — a whole GenomeTools Manual page, but make it bestie-friendly 💅

okay so. gt-cds lives in the GenomeTools Manual, and it's the little tool that adds CDS (coding sequence) features onto the exon features you already have sitting in a GFF3 file. that's the whole vibe. no cap. ✨

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✨ NAME ✨

gt-cds — add CDS (coding sequence) features to exon features given in a GFF3 file. 🧬💖

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🦋 SYNOPSIS 🦋

gt cds [option ...] [GFF3_file]

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💜 DESCRIPTION 💜

here's the tea, bestie: you've got exon features in a GFF3_file, and this tool is gonna add CDS features to them. and there are so many knobs to twiddle. let's go one by one, no skipping, we don't do skipping here. 🫶

• -minorflen [value] — sets the minimum length an open reading frame (ORF) must have to be added as a CDS feature, measured in amino acids. default: 64. 🍓
• -startcodon [yes|no] — require that an ORF must begin with a start codon. default: no. (so like, by default she is NOT requiring it, just so we're clear 👀)
• -finalstopcodon [yes|no] — require that the final ORF must end with a stop codon. default: no.
• -seqfile [filename] — set the sequence file from which to take the sequences. default: undefined. 🌸
• -encseq [filename] — set the encoded sequence indexname from which to take the sequences. default: undefined.
• -seqfiles — set the sequence files from which to extract the features; use -- to terminate the list of sequence files. 💀 (yes, the double dash. do not forget the double dash.)
• -matchdesc [yes|no] — search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match. default: no.
• -matchdescstart [yes|no] — exactly match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) from the beginning to the first whitespace. default: no. ✨
• -usedesc [yes|no] — use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries. if a description contains a sequence range (e.g., III:1000001..2000000), the first part is used as sequence ID (III) and the first range position as offset (1000001). default: no. 🔥
• -regionmapping [string] — set file containing sequence-region to sequence file mapping. default: undefined. (more on this file's format down below, keep scrolling 🧚)
• -v [yes|no] — be verbose. default: no. (she talks more. iconique.)
• -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.

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📁 File format for option -regionmapping 📁

the file you hand to the -regionmapping option defines a "mapping". and what does a mapping do? it maps the sequence-region entries given in the GFF3_file to a sequence file containing the corresponding sequence. simple as that, bestie. 🌈

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 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, which has to return the sequence file name when it is called with the sequence_region as argument. both valid, both slay. 💅

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🐞 REPORTING BUGS 🐞

found a bug? don't suffer in silence, report it to https://github.com/genometools/genometools/issues. 💌

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and that's the whole page, periodt. 🫶 this little masterpiece is GenomeTools 1.6.6, dated 11/09/2025, and honestly? she ate. ✨💖🎀