[ensembl-dev] fetch_nearest_Gene_by_Feature

[Fiona Nielsen]

Hi Ensembl team,

I am implementing a function using
gene_adaptor->fetch_nearest_Gene_by_Feature, but I am getting some
strange results.

After generating a Feature object for the position I am interested in,
I call fetch_nearest_Gene_by_Feature. Looking at the output I do
indeed retrieve a Gene object per Feature, but I can tell from the
location of the gene (and double checking in the genome browser) that
it is not the closest gene to the Feature position. See output example
below the code.

How should I interpret this output if it is not the nearest gene?
Am I giving the wrong input to the function?

Any help to solve this mystery is appreciated.

thanks,

-Fiona-

*** code snip ***
    my $BPslice =
$slice_adaptor->fetch_by_region('chromosome',$chr,$BP1pos,$BP1pos+1);
    my $feat = new Bio::EnsEMBL::Feature(
                                         -start  => $BP1pos,
                                         -end    => $BP1pos,
                                         -strand => 1,
                                         -slice  => $BPslice,
                                        );
    print "searching for nearest gene to: $BP1chr $BP1pos\n";

    my $BP1genelist =
$gene_adaptor->fetch_nearest_Gene_by_Feature($feat); #searching
downstream (-1)
    while( $BP1gene = pop(@{$BP1genelist})) {
      print $BP1gene->stable_id(). ":". $BP1gene->external_name().":".
$BP1gene->seq_region_name().":". $BP1gene->seq_region_start().":".
$BP1gene->seq_region_end().":". $BP1gene->strand()."\n";
    }
*** end code snip ***

*** output example ***
searching for nearest gene to: chr14 1085552
ENSG00000215398:RP11-754I20.1:14:19109939:19118336:1
searching for nearest gene to: chr14 20085552
ENSG00000258526:RP11-111A21.1:14:39944044:39982984:1
searching for nearest gene to: chr14 20182101
ENSG00000258526:RP11-111A21.1:14:39944044:39982984:1
searching for nearest gene to: chr14 52832186
ENSG00000185024:BRF1:14:105675623:105781926:-1
searching for nearest gene to: chr14 82832186
ENSG00000253303:IGHVIII-82:14:107287770:107288019:-1
searching for nearest gene to: chr14 101536162
ENSG00000253303:IGHVIII-82:14:107287770:107288019:-1
searching for nearest gene to: chr14 112907975
ENSG00000253303:IGHVIII-82:14:107287770:107288019:-1
searching for nearest gene to: chr14 252907975
ENSG00000253303:IGHVIII-82:14:107287770:107288019:-1
*** end output example ***


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