ucsc_genes2gff.pl - Convert UCSC Genome Browser-format gene files into GFF files
suitable for loading into gbrowse
% uscsc_genes2gff.pl [options] ucsc_file1 ucsc_file2...
Options:
-src <string> Choose a source for the gene, default "UCSC"
-origin <integer> Choose a relative position to number from, default
is "1"
This script massages the gene files available from the "tables" link
of the UCSC genome browser (genome.ucsc.edu) into a form suitable for loading
of gbrowse. Warning: it only works with the gene tables. Other tables, such as
EST alignments, contours and repeats, have their own formats which will
require other scripts to parse.
To use this script, get one or more UCSC tables, either from the
"Tables" link on the browser, or from the UCSC Genome Browser FTP
site. Give the table file as the argument to this script. You may want to
provide an alternative "source" field. Otherwise this script
defaults to "UCSC".
% pucsc_genes2gff.pl -src RefSeq refseq_data.ucsc > refseq.gff
The resulting GFF file can then be loaded into a Bio::DB::GFF database using the
following command:
% bulk_load_gff.pl -d <databasename> refseq.gff
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
Lincoln Stein <
[email protected]>.
Copyright (c) 2003 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.