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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'>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!<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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<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'>
dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Oliver, Gavin<br>
<b><span style='font-weight:bold'>Sent:</span></b> 24 November 2010 14:25<br>
<b><span style='font-weight:bold'>To:</span></b> dev<br>
<b><span style='font-weight:bold'>Subject:</span></b> [ensembl-dev] Problem
with core script</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=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hi, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I have a relatively straightforward script I use for pulling
gene annotation from the core database.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>The problem is it seems to have stopped working suddenly and
I can’t figure out why.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>The problem is occurring in the final line of this code.
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'># Set up gene, transcript and go adaptors<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>my $goadaptor = $registry->get_adaptor('Multi',
'Ontology', 'GOTerm');<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>my $gene_adaptor = $registry->get_adaptor( 'Human',
'Core', 'Gene' );<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>my $transcript_adaptor = $registry->get_adaptor('Human',
'Core', 'Transcript');<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'># Get list of all genes<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>my @genearray = @{$gene_adaptor->list_stable_ids()};<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'># Set up hash for storage of annotation<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>my %hash=();<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'># Foreach gene pull annotation<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>foreach my $geneid (@genearray) {<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>print "Pulling gene level annotation for $geneid...\n\n";<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> my $gene =
$gene_adaptor->fetch_by_stable_id($geneid);<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> my $slicekaryo =
$gene->slice->get_all_KaryotypeBands->[0];<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>The output looks like this:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Pulling gene level annotation for ENSG00000000003...
(executes ok)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Pulling gene level annotation for TSPAN6-002...<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>TSPAN6-002<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Can't call method "slice" on an undefined value at
./GeneTransProtRework.pl line 113.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>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?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Gavin Oliver, MSc<o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Team Leader Genomic
Research<o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
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<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Diagnostics<o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Tel: +44 (0)28
38395792<o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Fax: +44 (0)28
38398676<o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Visit our website
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<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><strong><b><font size=3 color=blue face="Times New Roman"><span
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lang=EN-GB style='font-size:12.0pt;color:black;font-weight:bold'><o:p> </o:p></span></font></b></p>
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<p class=MsoNormal><b><font size=3 color=black face="Times New Roman"><span
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