NAME

bp_process_sgd.pl - Massage SGD annotation flat files into a version suitable for the Generic Genome Browser

SYNOPSIS

% bp_process_sgd.pl chromosomal_features.tab > yeast.gff

DESCRIPTION

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:

% bp_process_sgd.pl chromosomal_features.tab > yeast.gff

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

AUTHOR

Lincoln Stein, lstein@cshl.org

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.

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