GT-ID_TO_MD5(1)

💅 GT-ID_TO_MD5 — it's from the GenomeTools Manual, bestie

✨ NAME ✨

okay so gt-id_to_md5 — what it does is it goes into the GFF3 files you hand it and swaps out the sequence IDs for MD5 fingerprints of the sequences they actually correspond to. that's the whole gig. slay.

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🌸 SYNOPSIS 🌸

gt id_to_md5 [option ...] [GFF3_file ...]

like. give it some options, give it some GFF3 files, and it does the thing. periodt.

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🦋 DESCRIPTION 🦋

here's the rundown, no cap:

🎀 the options, all of them, every single one 🎀

• -seqfile [filename] — points at the sequence file you want the sequences pulled from. default? undefined. so like, set it, bestie.
• -encseq [filename] — points at the encoded sequence indexname to take the sequences from instead. default: undefined.
• -seqfiles — sets the sequence files that the features get extracted from. and listen: you gotta use -- to terminate the list of sequence files, okay? don't forget.
• -matchdesc [yes|no] — this one goes digging through the sequence descriptions in your input files looking for the sequence IDs you want (the ones in the GFF3), and it reports the first match it finds. default: no.
• -matchdescstart [yes|no] — same vibe but stricter: it matches the sequence descriptions from the input files against the desired sequence IDs (in GFF3) exactly, going 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. and if a description has a sequence range in it (like, say, III:1000001..2000000), then 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.
• -subtargetids [yes|no] — swaps the target IDs out for MD5 sums. default: yes.
• -v [yes|no] — be verbose. spill the tea. default: no.
• -o [filename] — redirects the output into the file you name. default: undefined.
• -gzip [yes|no] — writes the output file gzip compressed. default: no.
• -bzip2 [yes|no] — writes the output file bzip2 compressed. default: no.
• -force [yes|no] — forces writing to the output file. default: no.
• -help — shows help and dips out.
• -version — shows version info and dips out.

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🧚 file format for option -regionmapping 🧚

so the file you feed to -regionmapping defines a “mapping”. and a mapping is literally just: it maps the sequence-region entries given in the GFF3_file to a sequence file that holds the matching sequence. you can define mappings in one of two forms, and here they are, verbatim, don't touch:

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

orrrrr:

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

the first form defines a Lua (<http://www.lua.org>) table called “mapping” that maps every sequence region to its corresponding sequence file. the second form defines a Lua function called “mapping”, and that function has to return the sequence file name whenever it gets called with the sequence_region as its argument. iykyk.

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😭 REPORTING BUGS 😭

found a bug? go tell on them at <https://github.com/genometools/genometools/issues>. they wanna know fr fr.

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🫶 and that's the whole page, bestie. you ate. go md5 some sequence IDs. 💖

sign-off time: this iconic little page is from GenomeTools 1.6.6, dated 11/09/2025. mwah. 💅✨