[ensembl-dev] [SPAM] - Re: Problem with core script - Email found in subject

[Oliver, Gavin]

Oh god.

I hang my head in shame.

Maybe I did change this script after all.  

2nd use of the name genearray.

Schoolboy error.



-----Original Message-----
From: Andreas Kahari [mailto:ak at ebi.ac.uk] 
Sent: 24 November 2010 15:29
To: Oliver, Gavin
Cc: dev
Subject: [SPAM] - Re: [ensembl-dev] Problem with core script - Email found in subject

On Wed, Nov 24, 2010 at 02:38:59PM -0000, Oliver, Gavin wrote:
> 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!


The code that you posted has a foreach loop that is not closed properly,
so I assume that you have omitted some code from the end of it.  Does
that code by any chance write things into the @genearray list that
you're iterating over?

If so, please consider using another list for that data as looping over
a changing list messes with my head.


Cheers,
Andreas

> 
>  
> 
> ________________________________
> 
> 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
> 
> Tel: +44 (0)28 38395792
> 
> Fax: +44 (0)28 38398676
> 
> Visit our website at: http://www.almacgroup.com
> <http://www.almacgroup.com/> 
> 
>  
> 
>   
> 
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>  
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-- 
Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, United Kingdom
 Kingdom