<div dir="ltr">Hi Stuart,<div><br></div><div>Apologies, I tweaked this bit of code for v75 and made a typo which causes this error.</div><div><br></div><div>I've fixed up the code on GitHub - if you re-download the VEP archive or git pull in the ensembl-tools directory (if you used git to get it) you should get the fixed version.</div>
<div><br></div><div>You could also just download this file over the top of your existing <a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a> script:</div><div><br></div><div><a href="https://github.com/Ensembl/ensembl-tools/blob/release/75/scripts/variant_effect_predictor/variant_effect_predictor.pl">https://github.com/Ensembl/ensembl-tools/blob/release/75/scripts/variant_effect_predictor/variant_effect_predictor.pl</a><br>
</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 31 March 2014 17:04, Stuart Watt <span dir="ltr"><<a href="mailto:Stuart.Watt@oicr.on.ca" target="_blank">Stuart.Watt@oicr.on.ca</a>></span> wrote:<br>
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Has something changed with the VEP options for —sift and —polyp hen when run offline?
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<div>I’m getting "INFO: --sift is not available for this species” message (same for polyphen) when I use it. </div>
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<div>Culpable lines appear to be (from #1833):</div>
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<div style="margin:0px;font-family:Menlo"> my $string = 'config_'.$tool.'_version';</div>
<div style="margin:0px;font-family:Menlo;min-height:14px"> if(!defined($config->{$string}) && !defined($config->{offline})) {</div>
<div style="margin:0px;font-family:Menlo"> my $var_mca = $config->{reg}->get_adaptor($config->{species}, 'variation', 'metacontainer');</div>
<div style="margin:0px;font-family:Menlo"> my $values = $var_mca->list_value_by_key($tool.'_version') if defined($var_mca);</div>
<div style="margin:0px;font-family:Menlo"> $config->{$string} = $values->[0] if $values && scalar @$values;</div>
<div style="margin:0px;font-family:Menlo"> }</div>
<div style="margin:0px;font-family:Menlo;min-height:14px"><br>
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<div style="margin:0px;font-family:Menlo"> if(!defined($config->{$string})) {</div>
<div style="margin:0px;font-family:Menlo"> debug("INFO: --$tool is not available for this species") unless defined($config->{quiet});</div>
<div style="margin:0px;font-family:Menlo"> delete $config->{$tool};</div>
<div style="margin:0px;font-family:Menlo"> }</div>
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<div style="margin:0px;font-family:Menlo"><br>
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<div>Because <span style="font-family:Menlo">$config->{config_sift_version} </span>is never set anywhere, this simply falls through the first condition into the second, removing the setting.</div>
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<div>When ran this in the debugger and manually set <span style="font-family:Menlo">$config->{config_sift_version}</span> and <span style="font-family:Menlo">$config->{config_polyphen_version}</span> , all seemed to work fine. It seems they should either
be set somehow, or be not required. Or maybe the first condition is supposed to test for <span style="font-family:Menlo">defined($config->{$tool})</span> instead. </div>
<div><br>
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<div>I don’t know the innards of the config setup here, but any advice would be welcome. </div>
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<div>All the best</div>
<div>Stuart</div>
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