Christopher Fields > BioPerl-1.6.901 > process_sgd.pl

Download:
BioPerl-1.6.901.tar.gz

Annotate this POD

CPAN RT

New  9
Open  4
View/Report Bugs
Source  

NAME ^

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

SYNOPSIS ^

  % 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:

  % 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

SEE ALSO ^

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

AUTHOR ^

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.

syntax highlighting: