[ensembl-dev] [SPAM] - Re: Problem with core script - Email found in subject
Andreas Kahari
ak at ebi.ac.uk
Wed Nov 24 16:06:59 GMT 2010
(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.
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> > Diagnostics Limited, registered no. NI043067. All preceding companies
> > are registered in Northern Ireland with a registered office address of
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> >
> >
> >
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> >
> >
> >
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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
>
--
Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, United Kingdom
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