BP_PROCESS_SGD(1p)

💖 NAME 💖

okay bestie, say hi to bp_process_sgd.pl ✨ — she takes those SGD annotation flat files and massages them into a version that's actually usable by the Generic Genome Browser. glow-up.exe fr fr 💅

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🦋 SYNOPSIS 🦋

% bp_process_sgd.pl chromosomal_features.tab > yeast.gff

that's it. that's the whole vibe. 🎀

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🌸 DESCRIPTION 🌸

so like, this script takes the SGD sequence annotation flat files living at ftp://genome-ftp.stanford.edu/pub/yeast/data_dump/feature/chromosomal_features.tab and turns them into a version of the GFF format that the generic genome browser can actually display. it's giving translator, it's giving bridge, it's giving i make the formats talk to each other 🫶

to use her, grab the SGD chromosomal_features.tab file from that FTP site up there 👆 and run this:

% bp_process_sgd.pl chromosomal_features.tab > yeast.gff

then — and this is the part where it gets iconic — your yeast.gff file can be loaded into a Bio::DB::GFF database with this:

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

note the <databasename> placeholder, bestie, that's a you problem, you fill it in 💀

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⭐ SEE ALSO ⭐

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

go read those too, no cap, they're the rest of the lore 📚

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👑 AUTHOR 👑

Lincoln Stein, lstein@cshl.org — king behavior honestly 🫡

Copyright (c) 2002 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.

okay so important: same terms as Perl itself, and if you want the warranty disclaimers they live in DISCLAIMER.txt — go look, don't assume, fr fr 🙈

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and that's the whole page, bestie 💜 this was BP_PROCESS_SGD(1p) from the User Contributed Perl Documentation, perl v5.32.1, dated 2021-08-15 — slay, go annotate some yeast 🧚✨