UCSC_GENES2GFF(1p)

📦
version 2.56 · 5 versions
, in ubuntu questing

💖 UCSC_GENES2GFF — bestie edition 💖

okay so this is the manual for ucsc_genes2gff.pl, from the UCSC_GENES2GFF(1p) page, and honestly? it's giving "tiny script, huge glow-up." she takes UCSC Genome Browser gene files and turns them into GFF files that gbrowse can actually load. no cap. 🧚

✨ NAME ✨

ucsc_genes2gff.pl — Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse.

like. that's her whole job. and she ate. 💅

🌸 SYNOPSIS 🌸

% uscsc_genes2gff.pl [options] ucsc_file1 ucsc_file2...

(yes bestie, that's the spelling in the original, uscsc and all — we don't fix it, we respect it 💀)

Options:

  • -src <string> — Choose a source for the gene, default "UCSC"
  • -origin <integer> — Choose a relative position to number from, default is "1"

🦋 DESCRIPTION 🦋

This script massages the gene files available from the "tables" link of the UCSC genome browser (genome.ucsc.edu) into a form suitable for loading of gbrowse. 💆‍♀️

⚠️ Warning, babe: it only works with the gene tables. Other tables, such as EST alignments, contours and repeats, have their own formats which will require other scripts to parse. so like. don't come for her with an EST alignment and expect magic. she will simply not. 🙈

To use this script, get one or more UCSC tables, either from the "Tables" link on the browser, or from the UCSC Genome Browser FTP site. Give the table file as the argument to this script. You may want to provide an alternative "source" field. Otherwise this script defaults to "UCSC". 👑

like, here's the vibe:

% pucsc_genes2gff.pl -src RefSeq refseq_data.ucsc > refseq.gff

(again — pucsc, exactly as written. she contains multitudes. 💖)

The resulting GFF file can then be loaded into a Bio::DB::GFF database using the following command:

% bulk_load_gff.pl -d <databasename> refseq.gff

and then boom. loaded. main character energy fr fr. 🔥

👀 SEE ALSO 👀

  • Bio::DB::GFF
  • bulk_load_gff.pl
  • load_gff.pl

💜 AUTHOR 💜

Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2003 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.

like, free software, same terms as Perl itself — iconic behaviour honestly. 🫶

and that's the whole page bestie!! this was perl v5.40.0, dated 2024-10-20, and the page is UCSC_GENES2GFF(1p) — mwah, go convert some genes, you've got this 💖✨🎀

📦 where this page comes from