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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Got this one sorted Steve. Stupid mistake
on my behalf – forgot I had edited the script and used the same array
name twice.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> Steve Moss
[mailto:gawbul@gmail.com] <br>
<b><span style='font-weight:bold'>Sent:</span></b> 24 November 2010 17:48<br>
<b><span style='font-weight:bold'>To:</span></b> dev@ensembl.org; Oliver, Gavin<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: Problem with core
script (Oliver, Gavin)</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hi Gavin,<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Also, did you update to the version 60 Perl API?<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Cheers,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><br>
Steve<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On 24 November 2010 14:39, <<a href="mailto:dev-request@ensembl.org">dev-request@ensembl.org</a>>
wrote:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
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1. Problem with core script (Oliver, Gavin)<br>
2. Re: Problem with core script (Oliver, Gavin)<br>
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<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 <st1:country-region w:st="on">Northern Ireland</st1:country-region> with a
registered office address of Almac House, 20 Seagoe Industrial Estate, <st1:place
w:st="on"><st1:City w:st="on">Craigavon</st1:City>, <st1:PostalCode w:st="on">BT63
5QD</st1:PostalCode>, <st1:country-region w:st="on">UK</st1:country-region></st1:place>.<br>
<br>
Almac Sciences (<st1:country-region w:st="on">Scotland</st1:country-region>)
Limited, registered in <st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region>
no. SC154034.<br>
<br>
Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac Diagnostics
LLC, Almac Pharma Services LLC and Almac Sciences LLC are <st1:State w:st="on"><st1:place
w:st="on">Delaware</st1:place></st1:State> 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>
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------------------------------<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 <st1:country-region w:st="on"><st1:place w:st="on">Northern
Ireland</st1:place></st1:country-region> with a registered office address of<br>
Almac House, 20 Seagoe Industrial Estate, <st1:place w:st="on"><st1:City w:st="on">Craigavon</st1:City>,
<st1:PostalCode w:st="on">BT63 5QD</st1:PostalCode>, <st1:country-region
w:st="on">UK</st1:country-region></st1:place>.<br>
<br>
<br>
<br>
Almac Sciences (<st1:country-region w:st="on">Scotland</st1:country-region>)
Limited, registered in <st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region>
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>
<st1:State w:st="on"><st1:place w:st="on">Delaware</st1:place></st1:State>
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>
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End of Dev Digest, Vol 5, Issue 35<br>
**********************************<o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><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><o:p></o:p></span></font></p>
</div>
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<P class=MsoNormal><FONT color=#000000><SPAN lang=EN-GB style="FONT-FAMILY: 'Times New Roman'">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.<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></FONT></P>
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<P class=MsoNormal style="mso-layout-grid-align: none"><FONT color=#0000ff><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Group (UK) Limited, registered no. NI061368.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Sciences Limited, registered no. NI041550.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Discovery Limited, registered no. NI046249. <SPAN style="mso-spacerun: yes"> </SPAN>Almac Pharma Services Limited, registered no. NI045055.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Clinical Services Limited, registered no. NI041905.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Clinical Technologies Limited, registered no. NI061202. <SPAN style="mso-spacerun: yes"> </SPAN>Almac Diagnostics Limited, registered no. NI043067.<SPAN style="mso-spacerun: yes"> </SPAN>All preceding companies are registered in <?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:country-region w:st="on">Northern Ireland</st1:country-region> with a registered office address of Almac House, 20 Seagoe Industrial Estate, <st1:place w:st="on"><st1:City w:st="on">Craigavon</st1:City>, <st1:PostalCode w:st="on">BT63 5QD</st1:PostalCode>, <st1:country-region w:st="on">UK</st1:country-region></st1:place>. <SPAN style="mso-spacerun: yes"> </SPAN><o:p></o:p></SPAN></FONT></P>
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<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Sciences (<st1:country-region w:st="on">Scotland</st1:country-region>) Limited, registered in <st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region> no. SC154034. <o:p></o:p></SPAN></P>
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<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">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">www.almacgroup.com</A><o:p></o:p></SPAN></P></SPAN></B></STRONG></FONT></body>
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