[ensembl-dev] gene count anomaly

[john samuel]

Hi,
I am trying to get an accurate count of all the ENSDARG genes from the 
latest zebrafish data (GRCz10) in ensembl.
If I use the perl api to get all the genes in all the chromosomes I get 
a total of 31,388 i.e.

my $slice_adaptor = $registry->get_adaptor( 'danio_rerio', 'Core', 
'Slice' );
my @slices = @{ $slice_adaptor->fetch_all('chromosome') };
my $total = 0;
my %all;
foreach my $slice (@slices) {
     my @genes = @{ $slice->get_all_Genes() };
     my $count = scalar @genes;
     $all{$slice->seq_region_name()}=$count;
     $total += $count;
}
foreach my $sorted (sort {$a<=>$b} keys %all) {
     print "chromosome: $sorted\t$all{$sorted}\n";
}
print "gene total is\t$total\n";

chromosome: MT    37
chromosome: 1    1386
chromosome: 2    1587
chromosome: 3    1611
chromosome: 4    3103
chromosome: 5    1704
chromosome: 6    1280
chromosome: 7    1507
chromosome: 8    1216
chromosome: 9    1108
chromosome: 10    1108
chromosome: 11    1039
chromosome: 12    952
chromosome: 13    1013
chromosome: 14    953
chromosome: 15    1146
chromosome: 16    1241
chromosome: 17    1048
chromosome: 18    942
chromosome: 19    1123
chromosome: 20    1253
chromosome: 21    1092
chromosome: 22    1174
chromosome: 23    1031
chromosome: 24    800
chromosome: 25    934
gene total is    31388

Anyone see anything wrong with how I get the total?  I don't, but then 
when I go to biomart (see below), I get a total of 31953



and if I go to the info page for the genome at 
http://useast.ensembl.org/Danio_rerio/Info/Annotation I see a 
differenttotal there too (31,650 not counting pseudogenes).



Anyone have any idea why the different totals and which one to believe 
and whether there's anything wrong with using the one that my code 
calculated as the definitive one?  I need to compare the total number of 
genes vs. the number that we are finding under certain conditions, to do 
some stats.
John



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