[ensembl-dev] Problem with core script

[Oliver, Gavin]

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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Fax: +44 (0)28 38398676

Visit our website at: http://www.almacgroup.com
<http://www.almacgroup.com/> 

 

  

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