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 Bio::Seq, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Seq

CPAN shell

perl -MCPAN -e shell
install Bio::Seq

For more information on module installation, please visit the detailed CPAN module installation guide.

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