process_sgd.pl - Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
% process_sgd.pl chromosomal_features.tab > yeast.gff
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 suitable for display by the generic genome browser.
To use this script, get the SGD chromosomal_features.tab file from the FTP site listed above, and run the following command:
The yeast.gff file can then be loaded into a Bio::DB::GFF database using the following command:
% bulk_load_gff.pl -d <databasename> yeast.gff
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
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.
To install CGI::Toggle, copy and paste the appropriate command in to your terminal.
cpanm
cpanm CGI::Toggle
CPAN shell
perl -MCPAN -e shell install CGI::Toggle
For more information on module installation, please visit the detailed CPAN module installation guide.