<div> </div>
<div>Hi Guillermo,</div>
<div> </div>
<div>If you paste the string from the error message into the interpro search you will get the result '(+) RNA virus helicase core domain (IPR027351)'. The '+' in the string will be interpreted as a special character unless you escape it. </div>
<div> </div>
<div>Try something like =~ /\Q$result\E/<br></div>
<div>Best wishes,</div>
<div> </div>
<div>Sarah<br></div>
<div class="gmail_quote">On Fri, Jun 7, 2013 at 7:23 AM, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div text="#000066" bgcolor="#FFFFFF">
<div>Hello,<br><br>Using my InterPro plugin I got this error i've never seen before:<br><br>Plugin 'Interpro' went wrong: Quantifier follows nothing in regex; marked by <-- HERE in m/(+ <-- HERE )RNA_virus_helicase_core_dom/ at ./vep_config/Plugins/Interpro.pm line 112.
<div class="im"><br><br>Here's Interpro plugin code:<a href="https://github.com/guillermomarco/vep_plugins_71/blob/master/Interpro.pm" target="_blank">https://github.com/guillermomarco/vep_plugins_71/blob/master/Interpro.pm</a><br>
<br></div>This seems wrong coding error with regex but there's no regex on that line: <br><br><span style="BORDER-BOTTOM:0px;BORDER-LEFT:0px;PADDING-BOTTOM:0px;TEXT-TRANSFORM:none;TEXT-INDENT:0px;MARGIN:0px;PADDING-LEFT:0px;PADDING-RIGHT:0px;FONT:bold 12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;LETTER-SPACING:normal;COLOR:rgb(51,51,51);BORDER-TOP:0px;BORDER-RIGHT:0px;WORD-SPACING:0px;PADDING-TOP:0px">if</span><span style="TEXT-TRANSFORM:none;TEXT-INDENT:0px;DISPLAY:inline!important;FONT:12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;FLOAT:none;LETTER-SPACING:normal;COLOR:rgb(51,51,51);WORD-SPACING:0px"> </span><span style="BORDER-BOTTOM:0px;BORDER-LEFT:0px;PADDING-BOTTOM:0px;TEXT-TRANSFORM:none;TEXT-INDENT:0px;MARGIN:0px;PADDING-LEFT:0px;PADDING-RIGHT:0px;FONT:12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;LETTER-SPACING:normal;COLOR:rgb(51,51,51);BORDER-TOP:0px;BORDER-RIGHT:0px;WORD-SPACING:0px;PADDING-TOP:0px">(</span><span>!</span><span style="BORDER-BOTTOM:0px;BORDER-LEFT:0px;PADDING-BOTTOM:0px;TEXT-TRANSFORM:none;TEXT-INDENT:0px;MARGIN:0px;PADDING-LEFT:0px;PADDING-RIGHT:0px;FONT:12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;LETTER-SPACING:normal;COLOR:rgb(0,128,128);BORDER-TOP:0px;BORDER-RIGHT:0px;WORD-SPACING:0px;PADDING-TOP:0px">$interpro_data</span><span style="BORDER-BOTTOM:0px;BORDER-LEFT:0px;PADDING-BOTTOM:0px;TEXT-TRANSFORM:none;TEXT-INDENT:0px;MARGIN:0px;PADDING-LEFT:0px;PADDING-RIGHT:0px;FONT:12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;LETTER-SPACING:normal;COLOR:rgb(51,51,51);BORDER-TOP:0px;BORDER-RIGHT:0px;WORD-SPACING:0px;PADDING-TOP:0px">[</span><span style="BORDER-BOTTOM:0px;BORDER-LEFT:0px;PADDING-BOTTOM:0px;TEXT-TRANSFORM:none;TEXT-INDENT:0px;MARGIN:0px;PADDING-LEFT:0px;PADDING-RIGHT:0px;FONT:12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;LETTER-SPACING:normal;COLOR:rgb(0,153,153);BORDER-TOP:0px;BORDER-RIGHT:0px;WORD-SPACING:0px;PADDING-TOP:0px">0</span><span style="BORDER-BOTTOM:0px;BORDER-LEFT:0px;PADDING-BOTTOM:0px;TEXT-TRANSFORM:none;TEXT-INDENT:0px;MARGIN:0px;PADDING-LEFT:0px;PADDING-RIGHT:0px;FONT:12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;LETTER-SPACING:normal;COLOR:rgb(51,51,51);BORDER-TOP:0px;BORDER-RIGHT:0px;WORD-SPACING:0px;PADDING-TOP:0px">]</span><span style="TEXT-TRANSFORM:none;TEXT-INDENT:0px;DISPLAY:inline!important;FONT:12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;FLOAT:none;LETTER-SPACING:normal;COLOR:rgb(51,51,51);WORD-SPACING:0px"> </span><span style="BORDER-BOTTOM:0px;BORDER-LEFT:0px;PADDING-BOTTOM:0px;TEXT-TRANSFORM:none;TEXT-INDENT:0px;MARGIN:0px;PADDING-LEFT:0px;PADDING-RIGHT:0px;FONT:bold 12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;LETTER-SPACING:normal;COLOR:rgb(51,51,51);BORDER-TOP:0px;BORDER-RIGHT:0px;WORD-SPACING:0px;PADDING-TOP:0px">&&</span><span style="TEXT-TRANSFORM:none;TEXT-INDENT:0px;DISPLAY:inline!important;FONT:12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;FLOAT:none;LETTER-SPACING:normal;COLOR:rgb(51,51,51);WORD-SPACING:0px"> </span><span style="BORDER-BOTTOM:0px;BORDER-LEFT:0px;PADDING-BOTTOM:0px;TEXT-TRANSFORM:none;TEXT-INDENT:0px;MARGIN:0px;PADDING-LEFT:0px;PADDING-RIGHT:0px;FONT:bold 12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;LETTER-SPACING:normal;COLOR:rgb(51,51,51);BORDER-TOP:0px;BORDER-RIGHT:0px;WORD-SPACING:0px;PADDING-TOP:0px">!</span><span style="BORDER-BOTTOM:0px;BORDER-LEFT:0px;PADDING-BOTTOM:0px;TEXT-TRANSFORM:none;TEXT-INDENT:0px;MARGIN:0px;PADDING-LEFT:0px;PADDING-RIGHT:0px;FONT:12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;LETTER-SPACING:normal;COLOR:rgb(0,128,128);BORDER-TOP:0px;BORDER-RIGHT:0px;WORD-SPACING:0px;PADDING-TOP:0px">$interpro_data</span><span style="BORDER-BOTTOM:0px;BORDER-LEFT:0px;PADDING-BOTTOM:0px;TEXT-TRANSFORM:none;TEXT-INDENT:0px;MARGIN:0px;PADDING-LEFT:0px;PADDING-RIGHT:0px;FONT:12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;LETTER-SPACING:normal;COLOR:rgb(51,51,51);BORDER-TOP:0px;BORDER-RIGHT:0px;WORD-SPACING:0px;PADDING-TOP:0px">[</span><span style="BORDER-BOTTOM:0px;BORDER-LEFT:0px;PADDING-BOTTOM:0px;TEXT-TRANSFORM:none;TEXT-INDENT:0px;MARGIN:0px;PADDING-LEFT:0px;PADDING-RIGHT:0px;FONT:12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;LETTER-SPACING:normal;COLOR:rgb(0,153,153);BORDER-TOP:0px;BORDER-RIGHT:0px;WORD-SPACING:0px;PADDING-TOP:0px">1</span><span style="BORDER-BOTTOM:0px;BORDER-LEFT:0px;PADDING-BOTTOM:0px;TEXT-TRANSFORM:none;TEXT-INDENT:0px;MARGIN:0px;PADDING-LEFT:0px;PADDING-RIGHT:0px;FONT:12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;LETTER-SPACING:normal;COLOR:rgb(51,51,51);BORDER-TOP:0px;BORDER-RIGHT:0px;WORD-SPACING:0px;PADDING-TOP:0px">])</span><span style="TEXT-TRANSFORM:none;TEXT-INDENT:0px;DISPLAY:inline!important;FONT:12px/18px Consolas,'Liberation Mono',Courier,monospace;WHITE-SPACE:pre-wrap;FLOAT:none;LETTER-SPACING:normal;COLOR:rgb(51,51,51);WORD-SPACING:0px"> </span><br>
<br>Guille.
<div>
<div class="h5"><br><br>On 05/17/2013 10:17 AM, Guillermo Marco Puche wrote:<br></div></div></div>
<blockquote type="cite">
<div>
<div class="h5">
<div>Hello Will,<br><br>That's seem very logic. But even if I advertise on my plugin I would like to hear the opinion from other devs.<br>I don't want people to use a plugin that isn't working properly or giving wrong information.<br>
<br>Thank you.<br><br>Best regards,<br>Guillermo.<br><br>On 05/17/2013 10:10 AM, Will McLaren wrote:<br></div>
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br></div>
<div>We're currently working on getting some official guidelines for external submissions of code in place.</div>
<div><br></div>
<div>Until that happens, we can't put plugins in the Ensembl VEP_plugins repo. However, feel free to advertise your plugins on your own GitHub, as you have done here!</div>
<div><br></div>
<div>Cheers</div>
<div><br></div>
<div>Will</div></div>
<div class="gmail_extra"><br><br>
<div class="gmail_quote">On 17 May 2013 08:22, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div text="#000066" bgcolor="#FFFFFF">
<div>Still waiting for someone answer before I can push it into VEP repo..
<div>
<div><br><br>On 05/15/2013 08:43 AM, Guillermo Marco Puche wrote:<br></div></div></div>
<div>
<div>
<blockquote type="cite">
<div>Hello,<br><br>Fixed a bug in script about empty Interpro_ac and idesc. <br>Git code updated: <a href="https://github.com/guillermomarco/vep_plugins_71/blob/master/Interpro.pm" target="_blank">https://github.com/guillermomarco/vep_plugins_71/blob/master/Interpro.pm</a><br>
<br>If someone give me the OK I'll push it to official VEP-plugin repository.<br><br>Best regards,<br>Guillermo.<br><br>On 05/14/2013 06:15 PM, Guillermo Marco Puche wrote:<br></div>
<blockquote type="cite">
<div>Hello,<br><br>I've come to this plugin: <a href="https://github.com/guillermomarco/vep_plugins_71/blob/master/Interpro.pm" target="_blank">https://github.com/guillermomarco/vep_plugins_71/blob/master/Interpro.pm</a><br>
<br>If you could check code and test it would be awesome !<br><br>I'm not 100% sure it's working perfectly.<br><br>Thank you.<br><br>Best regards,<br>Guillermo.<br><br>On 05/14/2013 03:38 PM, Will McLaren wrote:<br>
<br></div>
<blockquote type="cite">
<div dir="ltr">Hello,
<div><br></div>
<div>Ensembl contains domains mapped from multiple sources - often these will be the "same" domain with slightly different coordinates. Here you can see this on a typical transcript:</div>
<div><br></div>
<div><a href="http://www.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000128573;r=7:114055052-114333823;t=ENST00000403559" target="_blank">http://www.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000128573;r=7:114055052-114333823;t=ENST00000403559</a><br>
</div>
<div><br></div>
<div>You should also check the overlap of your variant with the domains, as you say using translation_start/end and $pf->start/end.</div>
<div><br></div>
<div>Regards</div>
<div><br></div>
<div>Will</div></div>
<div class="gmail_extra"><br><br>
<div class="gmail_quote">On 14 May 2013 14:16, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div text="#000066" bgcolor="#FFFFFF">
<div>Hello,<br><br>This makes a lot more sense.<br><br>There's something I still don't understand. For each variation i'm getting a lot of Interpro_ac and idesc.<br><br>Modified the code to debug but it stills not working since code is trying to print undefined values.<br>
<br>Should I compare and verify $tv->translation_start and $tv->translation_end with $pf->start and $pf->end to obtain the correct Interpro_ac and idesc?<br><br>Thank you,<br><br>Best regards.<span><font color="#888888"><br>
Guillermo.</font></span>
<div>
<div><br><br><br>On 05/14/2013 02:16 PM, Will McLaren wrote:<br></div></div></div>
<div>
<div>
<blockquote type="cite">
<div dir="ltr">$translation->get_all_ProteinFeatures();<br><br>returns an reference to an array of ProteinFeature objects. You'll need to iterate over them something like:<br><br>foreach my $pf(@{$translation->get_all_ProteinFeatures}) {<br>
$interpro{"INTERPRO_AC"} = $pf-> interpro_ac;<br> etc...<br>}<br><br>There is a mistake in the method docs that says it returns a single object, when actually it returns an arrayref.
<div><br>Regards<br><br>Will<br></div></div>
<div class="gmail_extra"><br><br>
<div class="gmail_quote">On 14 May 2013 12:44, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div text="#000066" bgcolor="#FFFFFF">
<div>Hello,<br><br>Here's Interpro plugin code: <a href="https://github.com/guillermomarco/vep_plugins_71/blob/master/Interpro.pm" target="_blank">https://github.com/guillermomarco/vep_plugins_71/blob/master/Interpro.pm</a><br>
<br>I'm getting unblessed reference error when trying to extract "interpro_ac" and "idesc" from my $pfeature object.<br><br>Here's a data dumper extract from $pfeature:<br><br><small><small>'Bio::EnsEMBL::ProteinFeature' ),<br>
bless( {<br> 'p_value' => '1.6e-42',<br> 'coverage' => undef,<br> 'percent_id' => '0',<br> 'adaptor' => $VAR1->[0]{'adaptor'},<br>
'hstrand' => undef,<br> 'idesc' => 'DH-domain',<br> 'hdescription' => undef,<br> 'slice' => undef,<br>
'dbname' => undef,<br> 'hspecies' => undef,<br> 'dbID' => '6415086',<br> 'strand' => 0,<br> 'seqname' => '936060',<br>
'translation_id' => '',<br> 'external_db_id' => undef,<br> 'db_display_name' => undef,<br> 'hend' => 0,<br>
'hcoverage' => undef,<br> 'score' => '0',<br> 'species' => undef,<br> 'interpro_ac' => 'IPR000219',<br>
'end' => 985,<br> 'analysis' => $VAR1->[0]{'analysis'}{'adaptor'}{'_logic_name_cache'}{'superfamily'},<br> 'hseqname' => 'SSF48065',<br>
'hstart' => 0,<br> 'extra_data' => undef,<br> 'group_id' => undef,<br> 'level_id' => undef,<br> 'start' => 803<br>
},</small></small><br><br>ERROR: Forked process failed<br>Plugin 'Interpro' went wrong: Can't call method "interpro_ac" on unblessed reference at /home/likewise-open/SGNET/gmarco/.vep/Plugins/Interpro.pm line 74
<div>
<div><br><br>On 05/13/2013 01:49 PM, Guillermo Marco Puche wrote:<br></div></div></div>
<div>
<div>
<blockquote type="cite">
<div>Ok I'm gonna give it a shot.<br>I installed latest API downloaded from Ensembl website on friday (10/05/2013) and I'm using a local Ensembl 71 database for VEP, no cache.<br><br>Best regards,<br>Guillermo<br>
<br>On 05/13/2013 01:45 PM, Will McLaren wrote:<br></div>
<blockquote type="cite">
<div dir="ltr">There was a bug in --domains when using the cache that has been recently fixed.
<div><br></div>
<div>Try updating your API and see if that's any better.</div>
<div><br></div>
<div>Will</div></div>
<div class="gmail_extra"><br><br>
<div class="gmail_quote">On 13 May 2013 12:38, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div text="#000066" bgcolor="#FFFFFF">
<div>Hello Will,<br><br>Yes I'm currently running VEP with --domains flag. It always shown empty for the testings for different samples I've done until now.<br>So domains flag is supposed to display the Interpro_ac for overlapping protein domains?<br>
<br>Best regards,<br>Guillermo.
<div>
<div><br><br>On 05/13/2013 01:34 PM, Will McLaren wrote:<br></div></div></div>
<div>
<div>
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>Have you tried the --domains flag in the VEP?</div>
<div><br></div>
<div>Perhaps this is not enough information for you but it does provide the display label of overlapping protein domains.</div>
<div><br></div>
<div>The protein object is referred to as a translation object in the Ensembl API; you can retrieve it from the transcript via $transcript->translation.</div>
<div><br></div>
<div>See <a href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Translation.html" target="_blank">http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Translation.html</a></div>
<div><br></div>
<div>Regards</div>
<div><br></div>
<div>Will</div></div>
<div class="gmail_extra"><br><br>
<div class="gmail_quote">On 13 May 2013 12:15, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div text="#000066" bgcolor="#FFFFFF">
<div>Hello,<br><br>So it seems nobody has done this yet. I'll do it then :)<br><br>Does VEP support any kind of """Proteinfeature"""? Checking the other scripts it seems I must be using Transcript feature_type. <br>
<br>Correct me if I'm wrong please, I'm a bit confused since interpro_ac is part from Core ProteinFeature. (EnsEMBL::ProteinFeature::interpro_ac)<br><br>Best regards,<br>Guillermo.
<div>
<div><br><br>On 05/09/2013 04:16 PM, Guillermo Marco Puche wrote:<br></div></div></div>
<blockquote type="cite">
<div>
<div>Hello,<br><br>Does anyone coded a plugin to obtain InterPro ID and description for VEP?<br>I've looked in VEP repo without luck.<br><br>I want to know before start coding.<br><br>Thank you !<br><br>Best regards,<br>
Guillermo.<br><br>
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