GT-SPLICESITEINFO(1)

🎀 NAME 🎀

gt-splicesiteinfo — she's the girl who shows you information about the splice sites you hand her in GFF3 files. that's it. that's the gig. and she ate. 💅

(and yes bestie, this whole thing lives in the GenomeTools Manual, so you're in the right place ✨)

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🌸 SYNOPSIS 🌸

gt splicesiteinfo [option ...] [GFF3_file ...]

okay so you call gt, you say splicesiteinfo, and then you sprinkle in as many options and as many GFF3_files as your heart desires. brackets mean "optional", bestie, so no pressure 🫶

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💅 DESCRIPTION 💅

here's the full option menu, and I mean full — every single one, no skimming, no skipping the "boring" ones, because they're literally all useful. periodt. 👑

• -seqfile [filename] — sets the sequence file she takes the sequences from. (default: undefined)
• -encseq [filename] — sets the encoded sequence indexname she takes the sequences from. (default: undefined)
• -seqfiles — sets the sequence files she extracts the features from. use -- to terminate the list of sequence files. 🦋
• -matchdesc [yes|no] — searches the sequence descriptions in the input files for the sequence IDs you want (the ones in GFF3) and reports the first match it finds. (default: no)
• -matchdescstart [yes|no] — matches those sequence descriptions from the input files against the sequence IDs you want (in GFF3) exactly, 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) onto the actual sequence entries. if a description has a sequence range in it (like, say, III:1000001..2000000), the first part becomes the sequence ID (III) and the first range position becomes the offset (1000001). (default: no)
• -regionmapping [string] — sets the file that contains the sequence-region to sequence-file mapping. (default: undefined)
• -addintrons [yes|no] — adds intron features in between the existing exon features (and she does this before computing the information to be shown). (default: no)
• -o [filename] — redirects the output to the file you name. (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)
• -help — displays help and exits. the classic. 🧚
• -version — displays version information and exits.

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🧚 File format for option -regionmapping 🧚

okay this part is lowkey the coolest. the file you hand to -regionmapping defines a "mapping". and what does a mapping do? it maps the sequence-region entries in your GFF3_file onto a sequence file that holds the corresponding sequence. ✨

you can define a mapping in one of these 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, form number one: you're defining a Lua (http://www.lua.org) table called "mapping", and it maps each sequence region to the sequence file that goes with it.

form number two: you're defining a Lua function called "mapping", and it has to return the sequence file name when it gets called with the sequence_region as its argument. iconic behaviour honestly 💜

also she's a Lua file, bestie — so mind your syntax, she will not forgive a stray comma 🙈

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😭 REPORTING BUGS 😭

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

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

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and that's the whole page, babe 🫶 go forth and inspect those splice sites, you absolute main character 👑

this was the GenomeTools manual, version 1.6.6, dated 11/09/2025 — mwah, stan, bye bestie 💖✨🎀🦋🌸💅