1.1   documentation

http://gmod.org/wiki/GFF3

http://search.cpan.org/~birney/bioperl-1.2.3/Bio/DB/GFF/Feature.pm

1.2   steps

1. if the last column of a non-chromosome line has 'ID' in it, find corresponding gene id using its value and add gene_symbol as 'Alias' and description as 'description'. Escape ; and , with %3B and %2C. code is variation/src/ImproveTAIRGeneGFF.py.

2. re-initialize and load the new GFF file into db by dazhe's init_db.pl and load.pl

3. add following configuration into arabidopsis1.conf:

   label   = sub {
                      my $feature = shift;
                      #my @aliases = $feature->aliases;
                      my @aliases = $feature->attributes('Alias');    #2009-2-4 both above and this works
                      #my @gene_symbol = $feature->attributes('gene_symbol');
                      #2009-2-4 gene_symbol is not built into the gbrowse search engine. but Alias is.
                      return "@aliases";
                      #return "@gene_symbol";
              }
   balloon hover   = sub {
              my $feature = shift;
              my $n = $feature->name();
              my $ref = $feature->seq_id();
              my $start = $feature->start();
              my $end = $feature->end();
              my @description = $feature->attributes("description");
              #my @notes = $feature->notes;   #if the description is put under 'Note'
              return "Protein Coding Gene: $n $ref:$start..$end.  @description";
              #return "@description";
              }
   

One tricky thing is that feature->attributes("xxx") returns an array (@) and array has to be wrapped within ", i.e. "@description".