<div dir="ltr">Hello,<div><br></div><div style>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 style><br></div><div style><a href="http://www.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000128573;r=7:114055052-114333823;t=ENST00000403559">http://www.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000128573;r=7:114055052-114333823;t=ENST00000403559</a><br>
</div><div style><br></div><div style>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 style><br></div><div style>Regards</div><div style>
<br></div><div style>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 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>
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 $pf->end to
obtain the correct Interpro_ac and idesc?<br>
<br>
Thank you,<br>
<br>
Best regards.<span class="HOEnZb"><font color="#888888"><br>
Guillermo.</font></span><div><div class="h5"><br>
<br>
<br>
On 05/14/2013 02:16 PM, Will McLaren wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr">$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 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>
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 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><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 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>
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