Hi Gavin,<div><br></div><div>Also, did you update to the version 60 Perl API?</div><div><br></div><div>Cheers,</div><div><br>Steve<br><br><div class="gmail_quote">On 24 November 2010 14:39, <span dir="ltr"><<a href="mailto:dev-request@ensembl.org">dev-request@ensembl.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Send Dev mailing list submissions to<br>
<a href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:dev-request@ensembl.org">dev-request@ensembl.org</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:dev-owner@ensembl.org">dev-owner@ensembl.org</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of Dev digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Problem with core script (Oliver, Gavin)<br>
2. Re: Problem with core script (Oliver, Gavin)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 24 Nov 2010 14:25:24 -0000<br>
From: "Oliver, Gavin" <<a href="mailto:gavin.oliver@almacgroup.com">gavin.oliver@almacgroup.com</a>><br>
Subject: [ensembl-dev] Problem with core script<br>
To: "dev" <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
Message-ID:<br>
<<a href="mailto:EBEA7CF8A45DD84797EADA312092799303880E10@NI-CR-SVC-EX1.pharms-services.com">EBEA7CF8A45DD84797EADA312092799303880E10@NI-CR-SVC-EX1.pharms-services.com</a>><br>
<br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hi,<br>
<br>
<br>
<br>
I have a relatively straightforward script I use for pulling gene<br>
annotation from the core database.<br>
<br>
<br>
<br>
The problem is it seems to have stopped working suddenly and I can't<br>
figure out why.<br>
<br>
<br>
<br>
The problem is occurring in the final line of this code.<br>
<br>
<br>
<br>
# Set up gene, transcript and go adaptors<br>
<br>
my $goadaptor = $registry->get_adaptor('Multi', 'Ontology', 'GOTerm');<br>
<br>
my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );<br>
<br>
my $transcript_adaptor = $registry->get_adaptor('Human', 'Core',<br>
'Transcript');<br>
<br>
<br>
<br>
# Get list of all genes<br>
<br>
my @genearray = @{$gene_adaptor->list_stable_ids()};<br>
<br>
<br>
<br>
# Set up hash for storage of annotation<br>
<br>
my %hash=();<br>
<br>
<br>
<br>
# Foreach gene pull annotation<br>
<br>
<br>
<br>
foreach my $geneid (@genearray) {<br>
<br>
print "Pulling gene level annotation for $geneid...\n\n";<br>
<br>
my $gene = $gene_adaptor->fetch_by_stable_id($geneid);<br>
<br>
<br>
<br>
my $slicekaryo = $gene->slice->get_all_KaryotypeBands->[0];<br>
<br>
<br>
<br>
The output looks like this:<br>
<br>
<br>
<br>
Pulling gene level annotation for ENSG00000000003... (executes ok)<br>
<br>
<br>
<br>
Pulling gene level annotation for TSPAN6-002...<br>
<br>
<br>
<br>
TSPAN6-002<br>
<br>
Can't call method "slice" on an undefined value at<br>
./GeneTransProtRework.pl line 113.<br>
<br>
<br>
<br>
<br>
<br>
I can't understand why it suddenly stopped working. I recently updated<br>
my databases to v60. Is it possible this had something to do with it?<br>
<br>
<br>
<br>
<br>
<br>
Gavin Oliver, MSc<br>
<br>
Team Leader Genomic Research<br>
<br>
Almac<br>
<br>
Diagnostics<br>
<br>
Tel: +44 (0)28 38395792<br>
<br>
Fax: +44 (0)28 38398676<br>
<br>
Visit our website at: <a href="http://www.almacgroup.com" target="_blank">http://www.almacgroup.com</a><br>
<<a href="http://www.almacgroup.com/" target="_blank">http://www.almacgroup.com/</a>><br>
<br>
<br>
<br>
<br>
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.<br>
<br>
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.<br>
<br>
Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034.<br>
<br>
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: <a href="http://www.almacgroup.com" target="_blank">www.almacgroup.com</a><br>
<br>
<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.ensembl.org/pipermail/dev/attachments/20101124/1452c1bd/attachment-0001.htm" target="_blank">http://lists.ensembl.org/pipermail/dev/attachments/20101124/1452c1bd/attachment-0001.htm</a>><br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Wed, 24 Nov 2010 14:38:59 -0000<br>
From: "Oliver, Gavin" <<a href="mailto:gavin.oliver@almacgroup.com">gavin.oliver@almacgroup.com</a>><br>
Subject: Re: [ensembl-dev] Problem with core script<br>
To: "Oliver, Gavin" <<a href="mailto:gavin.oliver@almacgroup.com">gavin.oliver@almacgroup.com</a>>, "dev"<br>
<<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
Message-ID:<br>
<<a href="mailto:EBEA7CF8A45DD84797EADA312092799303880E11@NI-CR-SVC-EX1.pharms-services.com">EBEA7CF8A45DD84797EADA312092799303880E11@NI-CR-SVC-EX1.pharms-services.com</a>><br>
<br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
I should point out that if I print the array of gene IDs, the second<br>
gene is ENSG00000000005 so I don't know where the TSPAN id is coming<br>
from!<br>
<br>
<br>
<br>
________________________________<br>
<br>
From: <a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a>] On Behalf<br>
Of Oliver, Gavin<br>
Sent: 24 November 2010 14:25<br>
To: dev<br>
Subject: [ensembl-dev] Problem with core script<br>
<br>
<br>
<br>
Hi,<br>
<br>
<br>
<br>
I have a relatively straightforward script I use for pulling gene<br>
annotation from the core database.<br>
<br>
<br>
<br>
The problem is it seems to have stopped working suddenly and I can't<br>
figure out why.<br>
<br>
<br>
<br>
The problem is occurring in the final line of this code.<br>
<br>
<br>
<br>
# Set up gene, transcript and go adaptors<br>
<br>
my $goadaptor = $registry->get_adaptor('Multi', 'Ontology', 'GOTerm');<br>
<br>
my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );<br>
<br>
my $transcript_adaptor = $registry->get_adaptor('Human', 'Core',<br>
'Transcript');<br>
<br>
<br>
<br>
# Get list of all genes<br>
<br>
my @genearray = @{$gene_adaptor->list_stable_ids()};<br>
<br>
<br>
<br>
# Set up hash for storage of annotation<br>
<br>
my %hash=();<br>
<br>
<br>
<br>
# Foreach gene pull annotation<br>
<br>
<br>
<br>
foreach my $geneid (@genearray) {<br>
<br>
print "Pulling gene level annotation for $geneid...\n\n";<br>
<br>
my $gene = $gene_adaptor->fetch_by_stable_id($geneid);<br>
<br>
<br>
<br>
my $slicekaryo = $gene->slice->get_all_KaryotypeBands->[0];<br>
<br>
<br>
<br>
The output looks like this:<br>
<br>
<br>
<br>
Pulling gene level annotation for ENSG00000000003... (executes ok)<br>
<br>
<br>
<br>
Pulling gene level annotation for TSPAN6-002...<br>
<br>
<br>
<br>
TSPAN6-002<br>
<br>
Can't call method "slice" on an undefined value at<br>
./GeneTransProtRework.pl line 113.<br>
<br>
<br>
<br>
<br>
<br>
I can't understand why it suddenly stopped working. I recently updated<br>
my databases to v60. Is it possible this had something to do with it?<br>
<br>
<br>
<br>
<br>
<br>
Gavin Oliver, MSc<br>
<br>
Team Leader Genomic Research<br>
<br>
Almac<br>
<br>
Diagnostics<br>
<br>
Tel: +44 (0)28 38395792<br>
<br>
Fax: +44 (0)28 38398676<br>
<br>
Visit our website at: <a href="http://www.almacgroup.com" target="_blank">http://www.almacgroup.com</a><br>
<<a href="http://www.almacgroup.com/" target="_blank">http://www.almacgroup.com/</a>><br>
<br>
<br>
<br>
<br>
<br>
The contents of this message and any attachments to it are confidential<br>
and may be legally privileged. If you have received this message in<br>
error, you should delete it from your system immediately and advise the<br>
sender.<br>
<br>
<br>
<br>
Almac Group (UK) Limited, registered no. NI061368. Almac Sciences<br>
Limited, registered no. NI041550. Almac Discovery Limited, registered<br>
no. NI046249. Almac Pharma Services Limited, registered no. NI045055.<br>
Almac Clinical Services Limited, registered no. NI041905. Almac<br>
Clinical Technologies Limited, registered no. NI061202. Almac<br>
Diagnostics Limited, registered no. NI043067. All preceding companies<br>
are registered in Northern Ireland with a registered office address of<br>
Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK.<br>
<br>
<br>
<br>
Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034.<br>
<br>
<br>
<br>
Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac<br>
Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are<br>
Delaware limited liability companies and Almac Group Incorporated is a<br>
Delaware Corporation. More information on the Almac Group can be found<br>
on the Almac website: <a href="http://www.almacgroup.com" target="_blank">www.almacgroup.com</a><br>
<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.ensembl.org/pipermail/dev/attachments/20101124/f63e42de/attachment.htm" target="_blank">http://lists.ensembl.org/pipermail/dev/attachments/20101124/f63e42de/attachment.htm</a>><br>
<br>
------------------------------<br>
<br>
_______________________________________________<br>
Dev mailing list<br>
<a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
<a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
<br>
<br>
End of Dev Digest, Vol 5, Issue 35<br>
**********************************<br>
</blockquote></div><br><br clear="all"><br>-- <br>Kindest regards,<br><br>Steve Moss<br><a href="http://stevemoss.ath.cx" target="_blank">http://stevemoss.ath.cx</a><br>
</div>