GMOD_SORT_GFF3(1p)

✨ NAME ✨

gmod_sort_gff3.pl — it sorts a GFF3 file so that lines with Parent tags land after their parent, no cap 💅

This one's a User Contributed Perl Documentation page, bestie, so you know it's community-made and community-loved 🫶

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🌸 SYNOPSIS 🌸

% gmod_sort_gff3.pl --infile <gff file name>

That's it. That's the whole vibe. One flag, one file, one sorted output 🎀

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💖 COMMAND-LINE OPTIONS 💖

• --infile — the name of the input gff3 file. Required. Like, genuinely required, she will not run without it bestie 🙈
• --outfile — the name of the output gff3 file. Defaults to sorted.gff if you don't say otherwise ✨

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🦋 DESCRIPTION 🦋

okay so. This is a very simple script — and the author is fully upfront that it's only lightly tested, which, respect for the honesty honestly 😭 — for sorting gff3 files.

The whole mission? Every line that has a Parent tag gets moved so it comes after the line that contains the parent's ID tag. Parent first, child after. Chronological. Correct. Iconic. 👑

Why do we care? Because files sorted this way are required for the GMOD chado bulk loader, gmod_bulk_load_gff3.pl. So if the bulk loader is throwing a fit at you, this little script is your main character moment 🧚

Heads up bestie: it's lightly tested, so give your output a lil vibe check before you feed it to anything important 💀

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💜 AUTHORS 💜

Scott Cain <cain@cshl.org> — the legend herself 🫶

Copyright (c) 2006

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. 🌈

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and that's the whole page!! 🎀 this doc came to you courtesy of perl v5.30.0, dated 2019-12-05, filed under the GMOD_SORT_GFF3(1p) manual section — slay, sort responsibly, and go make that bulk loader happy 💖✨