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

[Oliver, Gavin]

For some reason I totally overlooked the simple explanation and instead expended a lot of energy dreaming up mysql cache-type conspiracy theories.

:)

-----Original Message-----
From: Andreas Kahari [mailto:ak at ebi.ac.uk] 
Sent: 24 November 2010 16:07
To: Oliver, Gavin
Cc: dev
Subject: [SPAM] - Re: [SPAM] - Re: [ensembl-dev] Problem with core script - Email found in subject - Email found in subject

(phew!)


:-)


A


On Wed, Nov 24, 2010 at 03:41:03PM -0000, Oliver, Gavin wrote:
> 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/> 
> > 
> >  
> > 
> >   
> > 
> > The contents of this message and any attachments to it are confidential
> > and may be legally privileged. If you have received this message in
> > error, you should delete it from your system immediately and advise the
> > sender.
> > 
> >  
> > 
> > Almac Group (UK) Limited, registered no. NI061368.  Almac Sciences
> > Limited, registered no. NI041550.  Almac Discovery Limited, registered
> > no. NI046249.  Almac Pharma Services Limited, registered no. NI045055.
> > Almac Clinical Services Limited, registered no. NI041905.  Almac
> > Clinical Technologies Limited, registered no. NI061202.  Almac
> > Diagnostics Limited, registered no. NI043067.  All preceding companies
> > are registered in Northern Ireland with a registered office address of
> > Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK.  
> > 
> >  
> > 
> > Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034. 
> > 
> >  
> > 
> > Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac
> > Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are
> > Delaware limited liability companies and Almac Group Incorporated is a
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> > 
> 
> > _______________________________________________
> > Dev mailing list
> > Dev at ensembl.org
> > http://lists.ensembl.org/mailman/listinfo/dev
> 
> 
> -- 
> Andreas Kähäri, Ensembl Software Developer
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus
> Hinxton, Cambridge CB10 1SD, United Kingdom
>  Kingdom
> 

-- 
Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, United Kingdom
ed Kingdom