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<div class="moz-cite-prefix">Hello,<br>
<br>
Here's Interpro plugin code:
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
<a
href="https://github.com/guillermomarco/vep_plugins_71/blob/master/Interpro.pm">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<br>
<br>
On 05/13/2013 01:49 PM, Guillermo Marco Puche wrote:<br>
</div>
<blockquote cite="mid:5190D35D.2040709@sistemasgenomicos.com"
type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<div class="moz-cite-prefix">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
cite="mid:CAMVEDX19agczjuKajunb+b373fKxa2qPikr8yy_1WDf=uPCikA@mail.gmail.com"
type="cite">
<div dir="ltr">There was a bug in --domains when using the cache
that has been recently fixed.
<div><br>
</div>
<div style="">Try updating your API and see if that's any
better.</div>
<div style=""><br>
</div>
<div style="">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 moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000066">
<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 class="h5"><br>
<br>
On 05/13/2013 01:34 PM, Will McLaren wrote:<br>
</div>
</div>
</div>
<div>
<div class="h5">
<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 moz-do-not-send="true"
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
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000066">
<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>
<fieldset></fieldset>
<br>
</div>
</div>
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