GT-GFF3(1)

🦋 GT-GFF3 — the gff3 page, bestie edition ✨

okay so you wanna parse GFF3 files, maybe glow them up a lil, and spit them back out? that's gt-gff3, and she's a whole vibe. it's the gt gff3 tool from the GenomeTools manual, and i'm gonna walk you through every single flag like we're gossiping at lunch. no cap. 💅

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🌸 SYNOPSIS 🌸

gt gff3 [option ...] [GFF3_file ...]

that's it. that's the whole summoning ritual. feed her options, feed her GFF3 files, she does her thing. 🎀

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✨ DESCRIPTION ✨

every option, in order, nothing skipped, because we do NOT gatekeep here. 🫶

• -sort [yes|no] — sort the GFF3 features. heads up bestie, memory consumption is proportional to the input file size(s), so like, don't do this on a giant file and then act surprised. (default: no)
• -sortlines [yes|no] — sort the GFF3 features on a strict line basis. note: this is not sorted as defined by GenomeTools, it's just raw line vibes. (default: no)
• -sortnum [yes|no] — enable natural numeric sorting for sequence regions. also not sorted as defined by GenomeTools. (default: no)
• -tidy [yes|no] — try to tidy the GFF3 files up during parsing. lil cleanup moment. (default: no)
• -retainids [yes|no] — when available, use the original IDs provided in the source file. memory consumption is proportional to the input file size(s) again, so keep that in mind. (default: no)
• -checkids [yes|no] — make sure the ID attributes are unique within the scope of each GFF3_file, as required by the GFF3 specification. memory consumption is proportional to the input file size(s). and here's the tea: if features with the same Parent attribute are not separated by a # line, the GFF3 parser tries to treat them as a multi-line feature. this requires at least matching sequence IDs and types. (default: no)
• -addids [yes|no] — add missing ##sequence-region lines automatically. she's helpful like that. (default: yes)
• -fixregionboundaries [yes|no] — automatically adjust ##sequence-region lines to contain all their features. memory consumption is proportional to the input file size(s). (default: no)
• -addintrons [yes|no] — add intron features between existing exon features. cute lil filler features. (default: no)
• -offset [value] — transform all features by the given offset.
• -offsetfile [filename] — transform all features by the offsets given in file. (default: undefined)
• -setsource [string] — set the source value (2nd column) of each feature. (default: undefined)
• -typecheck [string] — use an ontology given in an OBO file to validate parent-child relationships. if no argument is given, the sofa.obo file from the gtdata/obo_files directory is used. if an argument is given, it is used as an OBO filename. in the case that such a file does not exist, .obo is added to the argument and loading the resulting filename from the gtdata/obo_files directory is attempted. (default: undefined)
• -xrfcheck [string] — check Dbxref and Ontology_term attributes for correct syntax according to a abbreviation definition file. if no argument is given, the GO.xrf_abbs file from the gtdata/xrf_abbr directory is used. if an argument is given, it is used as an specific filename for an abbreviation file. in the case that such a file does not exist, .xrf_abbr is added to the argument and loading the resulting filename from the gtdata/xrf_abbr directory is attempted. (default: undefined)
• -show [yes|no] — show GFF3 output. (default: yes)
• -v [yes|no] — be verbose. spill the tea, girl. (default: no)
• -width [value] — set output width for FASTA sequence printing (0 disables formatting). (default: 0)
• -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 -offsetfile 💖

okay this one needs its own lil moment because it's giving very specific. 🎀

the file supplied to option -offsetfile defines a mapping table named “offsets”. it maps the sequence-region entries given in the GFF3_file to offsets. it can be defined as follows:

offsets = {
  chr1  = 1000,
  chr2  = 500
}

when this example is used, all features with seqid “chr1” will be offset by 1000 and all features with seqid “chr2” by 500. periodt. 💅

⚠️ and listen: if -offsetfile is used, offsets for all sequence-regions contained in the given GFF3 files must be defined. no skipping, bestie, she will notice. 😭

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🐛 REPORTING BUGS 🐛

found a bug? don't suffer in silence, tell the devs. report bugs to https://github.com/genometools/genometools/issues. they wanna hear from you, fr fr. 🔥

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okay that's the whole page, you're officially a gt gff3 girlie now. this was the GenomeTools manual, version 1.6.6, dated 11/09/2025 — go forth and parse, you absolute icon. 👑🌈💜