[ensembl-dev] Problem with core script

[Andreas Kahari]

See below.

On Wed, Nov 24, 2010 at 02:25:24PM -0000, Oliver, Gavin wrote:
> Hi, 
> 
>  
> 
> I have a relatively straightforward script I use for pulling gene
> annotation from the core database.
> 
> The problem is it seems to have stopped working suddenly and I can't
> figure out why.
> 
> The problem is occurring in the final line of this code.  
> 

I've trimmed the code down a bit to the essentials (removeing the unused
GOTerm adaptor and the unused transcript adaptor, and the hash).

# Set up gene, transcript and go adaptors
my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );

# Get list of all genes
my @genearray = @{ $gene_adaptor->list_stable_ids() };

# Foreach gene pull annotation
foreach my $geneid (@genearray) {
  print "Pulling gene level annotation for $geneid...\n\n";

  my $gene       = $gene_adaptor->fetch_by_stable_id($geneid);
  my $slicekaryo = $gene->slice->get_all_KaryotypeBands->[0];
}


> The output looks like this:
> 
> Pulling gene level annotation for ENSG00000000003... (executes ok)
> Pulling gene level annotation for TSPAN6-002...

Hmm... Why would you suddenly get the display label of one of the
transcripts of gene ENSG00000000003 in @genearray?  There seems to be
some code missing.  The code above works for me on release 60.

> 
>  
> 
> TSPAN6-002
> 
> Can't call method "slice" on an undefined value at
> ./GeneTransProtRework.pl line 113.

No, because you failed to get the gene that has the stable ID
"TSPAN6-002" (there is no such Ensembl gene stable ID).

> I can't understand why it suddenly stopped working.  I recently updated
> my databases to v60.  Is it possible this had something to do with it?

I think there's code you're omitting to show us.


Cheers,
Andreas

> 
> Gavin Oliver, MSc
> 
> Team Leader Genomic Research
> 
> Almac
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-- 
Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, United Kingdom