BP_PROCESS_SGD(1)

📦 version 1.7.8, in nixos 26.05, nixpkgs unstable

✨ NAME ✨

bestie, you're looking at BP_PROCESS_SGD(1) — a User Contributed Perl Documentation page for bp_process_sgd.pl. this little script is here to massage SGD annotation flat files into a version suitable for the Generic Genome Browser, no cap 💅.

🎀 SYNOPSIS 🎀

% bp_process_sgd.pl chromosomal_features.tab > yeast.gff

💖 DESCRIPTION 💖

okay so this script massages the SGD sequence annotation flat files located at ftp://genome-ftp.stanford.edu/pub/yeast/data_dump/feature/chromosomal_features.tab into a version of the GFF format that's suitable for display by the generic genome browser. it's giving ✨ glow-up for flat files ✨.

to use this script, grab the SGD chromosomal_features.tab file from the FTP site listed above, then run this command:

% bp_process_sgd.pl chromosomal_features.tab > yeast.gff

then the yeast.gff file can be loaded into a Bio::DB::GFF database using this command:

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

🔥 SEE ALSO 🔥

go check out these icons:

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

👑 AUTHOR 👑

written by Lincoln Stein, lstein@cshl.org 🫶.

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 bestie, that's the whole page — cute sign-off time: perl v5.42.3, dated 2021-02-03, page BP_PROCESS_SGD(1). mwah 💋

📦 where this page comes from