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<div class="moz-cite-prefix">Hello,<br>
<br>
Fixed a bug in script about empty Interpro_ac and idesc. <br>
Git code updated:
<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>
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 cite="mid:51926325.1060301@sistemasgenomicos.com"
type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<div class="moz-cite-prefix">Hello,<br>
<br>
I've come to this plugin:
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
<a moz-do-not-send="true"
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>
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
cite="mid:CAMVEDX2qS58PV9gf84R+KstLCv5ZKpHQLuCeWGK8uXhXeSOSoQ@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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 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>
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
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>
Here's Interpro plugin code: <a
moz-do-not-send="true"
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
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><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
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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