NAME

       ucsc_genes2gff.pl - Convert UCSC Genome Browser-format gene files into GFF files suitable
       for loading into gbrowse

SYNOPSIS

         % 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"

DESCRIPTION

       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

SEE ALSO

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

AUTHOR

       Lincoln Stein <lstein@cshl.org>.

       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.