[ensembl-dev] Problem with core script (Oliver, Gavin)

[Steve Moss]

Hi Gavin,

Instead of the following:

*my @genearray = @{$gene_adaptor->list_stable_ids()};

*
*...*
*
# Foreach gene pull annotation*
*
foreach my $geneid (@genearray) {*
*
*
You could perhaps try this?

*foreach my $geneid (@{$gene_adaptor->list_stable_ids}) {*

Cheers,

Steve

>
> 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.
>
>
>
> # Set up gene, transcript and go adaptors
>
> my $goadaptor = $registry->get_adaptor('Multi', 'Ontology', 'GOTerm');
>
> my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
>
> my $transcript_adaptor = $registry->get_adaptor('Human', 'Core',
> 'Transcript');
>
>
>
> # Get list of all genes
>
> my @genearray = @{$gene_adaptor->list_stable_ids()};
>
>
>
> # Set up hash for storage of annotation
>
> my %hash=();
>
>
>
> # 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...
>
>
>
> TSPAN6-002
>
> Can't call method "slice" on an undefined value at
> ./GeneTransProtRework.pl line 113.
>
>
>
>
>
> 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?
>
>
>
>
>
> Gavin Oliver, MSc
>
> Team Leader Genomic Research
>
> Almac
>
> Diagnostics
>
> Tel: +44 (0)28 38395792
>
> Fax: +44 (0)28 38398676
>
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>
>
>
>
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-- 
Kindest regards,

Steve Moss
http://stevemoss.ath.cx
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