bp_process_sgd.pl - Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
% bp_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 BioPerl, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BioPerl
CPAN shell
perl -MCPAN -e shell install BioPerl
For more information on module installation, please visit the detailed CPAN module installation guide.