Hi Gavin,<div><br></div><div>The code you give works fine for me. Double check that you have all the correct APIs installed, and that your ensembl-variation API is the same version as the main ensembl API.</div><div><br></div>
<div>You could also see if there are any clues when you connect to the server, by adding the verbose option:</div><div><br></div><div><meta charset="utf-8"><p class="MsoNormal" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">
<font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">$registry->load_registry_from_db(</span></font></p><p class="MsoNormal" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">
<font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "> -host => '<a href="http://ensembldb.ensembl.org/" target="_blank">ensembldb.ensembl.org</a>',</span></font></p><p class="MsoNormal" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">
<font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "> -user => 'anonymous',</span></font></p><p class="MsoNormal" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">
<font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "> -port => 5306,</span></font></p><p class="MsoNormal" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">
<font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "> -verbose = > 1,</span></font></p><p class="MsoNormal" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">
<font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">);</span></font></p></div><div><br></div><div>If you're sure this is OK, try getting a variation adaptor:</div><div><br></div><div><meta charset="utf-8"><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; ">my $var_adaptor = $registry->get_adaptor("human", "variation", "variation");</span></div>
<div><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; "><br></span></div><div><font class="Apple-style-span" face="Arial">If this works but transcript variation doesn't, then try doing a fresh install of the ensembl-variation API module.</font></div>
<div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial">Will</font></div><div><br><div class="gmail_quote">On 21 February 2011 15:15, Oliver, Gavin <span dir="ltr"><<a href="mailto:gavin.oliver@almacgroup.com">gavin.oliver@almacgroup.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div lang="EN-US" link="blue" vlink="purple">
<div>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial">Hi, </span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial"> </span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial">I am trying to pull variations associated with a transcript
and am having a problem whereby the transcript variation adaptor is being
flagged as ‘undefined’.</span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial"> </span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial">I have tried to simplify the problem below.</span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial"> </span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial">my $registry = 'Bio::EnsEMBL::Registry';</span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial"> </span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial">$registry->load_registry_from_db(</span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial"> -host => '<a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a>',</span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial"> -user => 'anonymous',</span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial"> -port => 5306,</span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial">);</span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial"> </span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial">my $trv_adaptor =
$registry->get_adaptor("human", "variation",
"transcriptvariation"); </span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial"> </span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial">print $trv_adaptor;</span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial"> </span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial">This produces the error “Use of uninitialized value.”
for $trv_adaptor in the print command.</span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial"> </span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial">Why would $trv_adaptor be undefined at this stage?</span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial"> </span></font></p>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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