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Dear developers,<br>
<br>
I'm experiencing some VEP plugin errors on Ensembl 76+.<br>
<br>
I've uploaded both plugins failing to this public repository:
<a class="moz-txt-link-freetext" href="https://github.com/guillermomarco/vep_plugins">https://github.com/guillermomarco/vep_plugins</a><br>
<br>
I've been looking for API changes in
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1Utils_1_1BaseVepPlugin.html#a2d966d465a2bbc2a067417cc4978e304">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1Utils_1_1BaseVepPlugin.html#a2d966d465a2bbc2a067417cc4978e304</a>
but I can't really find why I'm getting the following errors:<br>
<br>
<pre>Plugin 'Interpro_fixed' went wrong: Can't call method "translation" on an undefined value at Interpro_fixed.pm line 107</pre>
<pre>Plugin 'Gene_description' went wrong: Can't call method "description" on an undefined value at Gene_description.pm line 78.
</pre>
It's like hashes are empty:<br>
<br>
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<table class="highlight tab-size-8 js-file-line-container"
style="box-sizing: border-box; border-collapse: collapse;
border-spacing: 0px; tab-size: 8; color: rgb(51, 51, 51);
font-family: Helvetica, arial, freesans, clean, sans-serif, 'Segoe
UI Emoji', 'Segoe UI Symbol'; font-size: 13.3333330154419px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: 12.1333341598511px; orphans:
auto; text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background: rgb(255, 255, 255);">
<tbody style="box-sizing: border-box;">
<tr style="box-sizing: border-box;">
<td id="LC77" class="blob-code js-file-line"
style="box-sizing: border-box; padding: 0px 10px; position:
relative; font-family: Consolas, 'Liberation Mono', Menlo,
Courier, monospace; font-size: 12px; color: rgb(51, 51, 51);
vertical-align: top; white-space: pre; overflow: visible;">
<span class="nv" style="box-sizing: border-box; color:
rgb(0, 128, 128);">$gene</span> <span class="o"
style="box-sizing: border-box; font-weight: bold;">=</span>
<span class="nv" style="box-sizing: border-box; color:
rgb(0, 128, 128);">$config</span><span class="o"
style="box-sizing: border-box; font-weight: bold;">-></span><span
class="p" style="box-sizing: border-box;">{</span><span
class="n" style="box-sizing: border-box; color: rgb(51,
51, 51);">ga</span><span class="p" style="box-sizing:
border-box;">}</span><span class="o" style="box-sizing:
border-box; font-weight: bold;">-></span><span
class="n" style="box-sizing: border-box; color: rgb(51,
51, 51);">fetch_by_transcript_stable_id</span><span
class="p" style="box-sizing: border-box;">(</span><span
class="nv" style="box-sizing: border-box; color: rgb(0,
128, 128);">$transcript_id</span><span class="p"
style="box-sizing: border-box;">);</span></td>
</tr>
<tr style="box-sizing: border-box;">
<td id="L78" class="blob-num js-line-number"
data-line-number="78" style="box-sizing: border-box;
padding: 0px 10px; width: 50px; min-width: 50px;
font-family: Consolas, 'Liberation Mono', Menlo, Courier,
monospace; font-size: 12px; line-height: 18px; color:
rgba(0, 0, 0, 0.298039); vertical-align: top; text-align:
right; border-style: solid; border-color: rgb(238, 238,
238); border-width: 0px 1px 0px 0px; cursor: pointer;
-webkit-user-select: none;"><br>
</td>
<td id="LC78" class="blob-code js-file-line"
style="box-sizing: border-box; padding: 0px 10px; position:
relative; font-family: Consolas, 'Liberation Mono', Menlo,
Courier, monospace; font-size: 12px; color: rgb(51, 51, 51);
vertical-align: top; white-space: pre; overflow: visible;">
<span class="nv" style="box-sizing: border-box; color:
rgb(0, 128, 128);">$gene_desc</span> <span class="o"
style="box-sizing: border-box; font-weight: bold;">=</span>
<span class="nv" style="box-sizing: border-box; color:
rgb(0, 128, 128);">$gene</span><span class="o"
style="box-sizing: border-box; font-weight: bold;">-></span><span
class="n" style="box-sizing: border-box; color: rgb(51,
51, 51);">description</span><span class="p"
style="box-sizing: border-box;">;</span></td>
</tr>
</tbody>
</table>
<br>
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<table class="highlight tab-size-8 js-file-line-container"
style="box-sizing: border-box; border-collapse: collapse;
border-spacing: 0px; tab-size: 8; color: rgb(51, 51, 51);
font-family: Helvetica, arial, freesans, clean, sans-serif, 'Segoe
UI Emoji', 'Segoe UI Symbol'; font-size: 13.3333330154419px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: 12.1333341598511px; orphans:
auto; text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background: rgb(255, 255, 255);">
<tbody style="box-sizing: border-box;">
<tr style="box-sizing: border-box;">
<td id="LC105" class="blob-code js-file-line"
style="box-sizing: border-box; padding: 0px 10px; position:
relative; font-family: Consolas, 'Liberation Mono', Menlo,
Courier, monospace; font-size: 12px; color: rgb(51, 51, 51);
vertical-align: top; white-space: pre; overflow: visible;">
<span class="k" style="box-sizing: border-box; font-weight:
bold;">my</span> <span class="nv" style="box-sizing:
border-box; color: rgb(0, 128, 128);">$slice_adaptor</span>
<span class="o" style="box-sizing: border-box; font-weight:
bold;">=</span> <span class="nv" style="box-sizing:
border-box; color: rgb(0, 128, 128);">$config</span><span
class="o" style="box-sizing: border-box; font-weight:
bold;">-></span><span class="p" style="box-sizing:
border-box;">{</span><span class="n" style="box-sizing:
border-box; color: rgb(51, 51, 51);">reg</span><span
class="p" style="box-sizing: border-box;">}</span><span
class="o" style="box-sizing: border-box; font-weight:
bold;">-></span><span class="n" style="box-sizing:
border-box; color: rgb(51, 51, 51);">get_adaptor</span><span
class="p" style="box-sizing: border-box;">((</span><span
class="nv" style="box-sizing: border-box; color: rgb(0,
128, 128);">$config</span><span class="o"
style="box-sizing: border-box; font-weight: bold;">-></span><span
class="p" style="box-sizing: border-box;">{</span><span
class="n" style="box-sizing: border-box; color: rgb(51,
51, 51);">species</span><span class="p" style="box-sizing:
border-box;">}),</span> <span class="s"
style="box-sizing: border-box; color: rgb(223, 80, 0);">'core'</span><span
class="p" style="box-sizing: border-box;">,</span> <span
class="s" style="box-sizing: border-box; color: rgb(223,
80, 0);">'Transcript'</span><span class="p"
style="box-sizing: border-box;">);</span></td>
</tr>
<tr style="box-sizing: border-box;">
<td id="L106" class="blob-num js-line-number"
data-line-number="106" style="box-sizing: border-box;
padding: 0px 10px; width: 50px; min-width: 50px;
font-family: Consolas, 'Liberation Mono', Menlo, Courier,
monospace; font-size: 12px; line-height: 18px; color:
rgba(0, 0, 0, 0.298039); vertical-align: top; text-align:
right; border-style: solid; border-color: rgb(238, 238,
238); border-width: 0px 1px 0px 0px; cursor: pointer;
-webkit-user-select: none;"><br>
</td>
<td id="LC106" class="blob-code js-file-line"
style="box-sizing: border-box; padding: 0px 10px; position:
relative; font-family: Consolas, 'Liberation Mono', Menlo,
Courier, monospace; font-size: 12px; color: rgb(51, 51, 51);
vertical-align: top; white-space: pre; overflow: visible;">
<span class="k" style="box-sizing: border-box; font-weight:
bold;">my</span> <span class="nv" style="box-sizing:
border-box; color: rgb(0, 128, 128);">$tr</span> <span
class="o" style="box-sizing: border-box; font-weight:
bold;">=</span> <span class="nv" style="box-sizing:
border-box; color: rgb(0, 128, 128);">$slice_adaptor</span><span
class="o" style="box-sizing: border-box; font-weight:
bold;">-></span><span class="n" style="box-sizing:
border-box; color: rgb(51, 51, 51);">fetch_by_stable_id</span><span
class="p" style="box-sizing: border-box;">(</span><span
class="nv" style="box-sizing: border-box; color: rgb(0,
128, 128);">$Transcript</span><span class="p"
style="box-sizing: border-box;">);</span></td>
</tr>
<tr style="box-sizing: border-box;">
<td id="L107" class="blob-num js-line-number"
data-line-number="107" style="box-sizing: border-box;
padding: 0px 10px; width: 50px; min-width: 50px;
font-family: Consolas, 'Liberation Mono', Menlo, Courier,
monospace; font-size: 12px; line-height: 18px; color:
rgba(0, 0, 0, 0.298039); vertical-align: top; text-align:
right; border-style: solid; border-color: rgb(238, 238,
238); border-width: 0px 1px 0px 0px; cursor: pointer;
-webkit-user-select: none;"><br>
</td>
<td id="LC107" class="blob-code js-file-line"
style="box-sizing: border-box; padding: 0px 10px; position:
relative; font-family: Consolas, 'Liberation Mono', Menlo,
Courier, monospace; font-size: 12px; color: rgb(51, 51, 51);
vertical-align: top; white-space: pre; overflow: visible;">
<span class="k" style="box-sizing: border-box; font-weight:
bold;">my</span> <span class="nv" style="box-sizing:
border-box; color: rgb(0, 128, 128);">$translation</span>
<span class="o" style="box-sizing: border-box; font-weight:
bold;">=</span> <span class="nv" style="box-sizing:
border-box; color: rgb(0, 128, 128);">$tr</span><span
class="o" style="box-sizing: border-box; font-weight:
bold;">-></span><span class="n" style="box-sizing:
border-box; color: rgb(51, 51, 51);">translation</span><span
class="p" style="box-sizing: border-box;">;</span></td>
</tr>
</tbody>
</table>
<br>
I suspect of <span class="nv" style="box-sizing: border-box; color:
rgb(0, 128, 128);">$config</span><span class="o"
style="box-sizing: border-box; font-weight: bold;">-></span><span
class="p" style="box-sizing: border-box;">{</span><span class="n"
style="box-sizing: border-box; color: rgb(51, 51, 51);">ga</span><span
class="p" style="box-sizing: border-box;">} and </span><span
class="nv" style="box-sizing: border-box; color: rgb(0, 128,
128);">$config</span><span class="o" style="box-sizing:
border-box; font-weight: bold;">-></span><span class="p"
style="box-sizing: border-box;">{</span><span class="n"
style="box-sizing: border-box; color: rgb(51, 51, 51);">reg</span><span
class="p" style="box-sizing: border-box;">} are the cause of this
problem, because I still see </span><span class="p"
style="box-sizing: border-box;"><span class="n" style="box-sizing:
border-box; color: rgb(51, 51, 51);"><span class="n"
style="box-sizing: border-box; color: rgb(51, 51, 51);">fetch_by_transcript_stable_id</span><span
class="p" style="box-sizing: border-box;"> and </span>fetch_by_stable_id</span><span
class="p" style="box-sizing: border-box;"></span> methods on
Ensembl API.<br>
<br>
Thanks !<br>
<br>
<br>
Best regards,<br>
Guillermo.<br>
</span>
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