BED2GFF3(1p)

💖 BED2GFF3(1p) — the manual, but make it cute 💖

okay bestie, gather round, because this is the BED2GFF3(1p) page and it's literally from the User Contributed Perl Documentation section, and it's about turning UCSC Genome Browser gene files into GFF files that gbrowse can actually eat. no cap. 🧬✨

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🌸 NAME 🌸

ucsc_genes2gff.pl — bestie, this script converts UCSC Genome Browser-format gene files into GFF files that are suitable for loading into gbrowse. that's the whole vibe. 👑

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✨ SYNOPSIS ✨

run it like this, okay?

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

and here are the options, they're giving very much minimal but mighty:

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

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🦋 DESCRIPTION 🦋

so what this script actually does: it massages the gene files you can grab from the "tables" link of the UCSC genome browser (genome.ucsc.edu) into a form suitable for loading into gbrowse. glow-up arc, honestly. ✨

warning tho, fr fr: 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 don't come for this script with an EST file, it will simply not eat. 😭

to use it, you get one or more UCSC tables — either from the "Tables" link on the browser, or from the UCSC Genome Browser FTP site. then you just hand the table file to this script as the argument. you may want to provide an alternative "source" field. otherwise this script defaults to "UCSC". 🎀

like so:

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

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

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

and that's it, that's the pipeline, main character energy from start to finish. 💜

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🌈 SEE ALSO 🌈

go read these too, iykyk:

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

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👑 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. 📜

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and that's the whole page, bestie!! this one shipped as part of perl v5.40.0, dated 2024-10-20, under the name BED2GFF3(1p) — go forth and convert those genes, you absolute icon 💖🌸✨