[ensembl-dev] Problem with core script (Oliver, Gavin)

Wed Nov 24 17:51:37 GMT 2010

Got this one sorted Steve.  Stupid mistake on my behalf - forgot I had
edited the script and used the same array name twice.

________________________________

From: Steve Moss [mailto:gawbul at gmail.com] 
Sent: 24 November 2010 17:48
To: dev at ensembl.org; Oliver, Gavin
Subject: Re: Problem with core script (Oliver, Gavin)

Hi Gavin,

Also, did you update to the version 60 Perl API?

Cheers,

Steve

On 24 November 2010 14:39, <dev-request at ensembl.org> wrote:

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Today's Topics:

  1. Problem with core script (Oliver, Gavin)
  2. Re: Problem with core script (Oliver, Gavin)

----------------------------------------------------------------------

Message: 1
Date: Wed, 24 Nov 2010 14:25:24 -0000
From: "Oliver, Gavin" <gavin.oliver at almacgroup.com>
Subject: [ensembl-dev] Problem with core script
To: "dev" <dev at ensembl.org>
Message-ID:

Content-Type: text/plain; charset="us-ascii"

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
Delaware Corporation.  More information on the Almac Group can be found
on the Almac website: www.almacgroup.com

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Message: 2
Date: Wed, 24 Nov 2010 14:38:59 -0000
From: "Oliver, Gavin" <gavin.oliver at almacgroup.com>
Subject: Re: [ensembl-dev] Problem with core script
To: "Oliver, Gavin" <gavin.oliver at almacgroup.com>,      "dev"
       <dev at ensembl.org>
Message-ID:

Content-Type: text/plain; charset="us-ascii"

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

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
Delaware Corporation.  More information on the Almac Group can be found
on the Almac website: www.almacgroup.com

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-- 
Kindest regards,

Steve Moss
http://stevemoss.ath.cx

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