[ensembl-dev] Problem with core script
Oliver, Gavin
gavin.oliver at almacgroup.com
Wed Nov 24 14:38:59 GMT 2010
I should point out that if I print the array of gene IDs, the second
gene is ENSG00000000005 so I don't know where the TSPAN id is coming
from!
________________________________
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf
Of Oliver, Gavin
Sent: 24 November 2010 14:25
To: dev
Subject: [ensembl-dev] Problem with core script
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
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