GT-SPECK(1)

💖 GT-SPECK(1) 💖

okay bestie, so this is the GenomeTools Manual page for gt-speck, and it's literally the vibe-checker for your GFF3 files. sit down, grab a boba, we're doing this 🧋✨

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🌸 NAME 🌸

gt-speck — Checks spec definition compliance in GFF3 input.

like, it looks at your GFF3 and goes "hmm, does this actually follow the spec bestie?" and tells you. no cap. 👑

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✨ SYNOPSIS ✨

gt speck [options] [GFF3_file ...]

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🦋 DESCRIPTION 🦋

so here's the whole menu of options, and there are a lot of them, but that's fine, we're built different. every single one is here, i'm not skipping a single crumb 🍓

• -specfile [filename] — the file with the specification definition (default: undefined). like the rulebook you're checking against.
• -colored [yes|no] — show colored output (default: yes). and yes obviously you want this, it's giving rainbow 🌈
• -provideindex [yes|no] — provide feature index in specfile namespace (requires O(n) memory for n input features) (default: no). heads up: it's lowkey hungry for memory, so know what you're doing 💅
• -sort [yes|no] — sort input before checking (requires O(n) memory for n input features) (default: no). also a memory girlie, same deal.
• -failhard [yes|no] — stop processing and report runtime errors instead of recording them in the results (default: no). dramatic mode: activated 💀
• -output [string] — output format, choose from: [json, text, html, statsonly, tabular] or give path to output driver (default: text). pick your aesthetic, there's one for every mood ✨
• -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: so)
• -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. don't forget the -- bestie, she's important 🫶
• -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). strict queen behavior, we love to see it 👑
• -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)
• -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)
• -v [yes|no] — be verbose (default: no). give me all the tea ☕
• -help — display help and exit
• -version — display version information and exit

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😭 REPORTING BUGS 😭

Report bugs to https://github.com/genometools/genometools/issues.

like please do actually tell them, they wanna know, fr fr 🙈

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ok and that's the whole page bestie, you ate that 💅✨

GenomeTools version 1.6.6, dated 11/09/2025 — shoutout to the whole GenomeTools crew, this page is theirs, i just did her makeup 💖 mwah, bye 🎀