<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000066">
<div class="moz-cite-prefix">Hello,<br>
<br>
In case someone is using my Interpro plugin for VEP be aware that
results are <b>NOT CORRECT.</b><br>
I'm getting Intepro reports for intron_variants which makes no
sense. <br>
<br>
ie:<br>
<br>
AKT1 chr14 105238820 G C ENSG00000142208
v-akt_murine_thymoma_viral_oncogene_homolog_1
ENST00000407796.2:c.1173-31C>G 11/13 - - intron_variant 0.0298
0.0041 0.02 0 0.07 <b>IPR001849 Pleckstrin_homology </b>- -
rs61761201 Transcript ENST00000407796 NM_001014431.1 CCDS9994.1 -
1.790<br>
<br>
Plugin code is located here:
<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>
I would really appreciate if someone could help me to fix this.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 06/10/2013 01:02 PM, Guillermo Marco Puche wrote:<br>
</div>
<blockquote cite="mid:51B5B254.2050000@sistemasgenomicos.com"
type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<div class="moz-cite-prefix">Heelo Laurent,<br>
<br>
I'll try and report back.<br>
<br>
Thank you very much.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 06/10/2013 11:47 AM, Laurent Gil wrote:<br>
</div>
<blockquote cite="mid:51B5A09D.507@ebi.ac.uk" type="cite">Hi
Guillermo, <br>
<br>
I think Sarah was alking about the line 115 of your plugin: <br>
<br>
elsif ($interpro_data[0] =~ /$interpro_ac/ ||
$interpro_data[1] =~ /$idesc/) { <br>
<br>
Where you need to replace the code "$interpro_data[1]
=~/$idesc/" by "$interpro_data[1] =~ /\Q$idesc\E/" <br>
<br>
<br>
Cheers, <br>
<br>
Laurent <br>
<br>
On 08/06/2013 09:06, <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>
wrote: <br>
<blockquote type="cite">I've been trying that but I don't know
exactly where to use =~ /\Q$result\E. <br>
I'm confused. <br>
<br>
I suppose when I save var $idesc <br>
<br>
<blockquote type="cite">Hi Guillermo, <br>
<br>
If you paste the string from the error message into the
interpro search <br>
you <br>
will get the result '(+) RNA virus helicase core domain
(IPR027351)'. The <br>
'+' in the string will be interpreted as a special character
unless you <br>
escape it. <br>
<br>
Try something like =~ /\Q$result\E/ <br>
Best wishes, <br>
<br>
Sarah <br>
On Fri, Jun 7, 2013 at 7:23 AM, Guillermo Marco Puche < <br>
<a moz-do-not-send="true" class="moz-txt-link-abbreviated"
href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>>
wrote: <br>
<br>
<blockquote type="cite"> 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; <br>
marked <br>
by <-- HERE in m/(+ <-- HERE
)RNA_virus_helicase_core_dom/ at <br>
./vep_config/Plugins/Interpro.pm line 112. <br>
<br>
<br>
Here's Interpro plugin code: <br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
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>
This seems wrong coding error with regex but there's no
regex on that <br>
line: <br>
<br>
if (!$interpro_data[0] && !$interpro_data[1]) <br>
<br>
Guille. <br>
<br>
<br>
On 05/17/2013 10:17 AM, Guillermo Marco Puche wrote: <br>
<br>
Hello Will, <br>
<br>
That's seem very logic. But even if I advertise on my
plugin I would <br>
like <br>
to hear the opinion from other devs. <br>
I don't want people to use a plugin that isn't working
properly or <br>
giving <br>
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>
<br>
Hi Guillermo, <br>
<br>
We're currently working on getting some official
guidelines for external <br>
submissions of code in place. <br>
<br>
Until that happens, we can't put plugins in the Ensembl
VEP_plugins <br>
repo. <br>
However, feel free to advertise your plugins on your own
GitHub, as you <br>
have done here! <br>
<br>
Cheers <br>
<br>
Will <br>
<br>
<br>
On 17 May 2013 08:22, Guillermo Marco Puche < <br>
<a moz-do-not-send="true" class="moz-txt-link-abbreviated"
href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>>
wrote: <br>
<br>
<blockquote type="cite"> Still waiting for someone answer
before I can push it into VEP repo.. <br>
<br>
<br>
On 05/15/2013 08:43 AM, Guillermo Marco Puche wrote: <br>
<br>
Hello, <br>
<br>
Fixed a bug in script about empty Interpro_ac and idesc.
<br>
Git code updated: <br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
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 <br>
repository. <br>
<br>
Best regards, <br>
Guillermo. <br>
<br>
On 05/14/2013 06:15 PM, Guillermo Marco Puche wrote: <br>
<br>
Hello, <br>
<br>
I've come to this plugin: <br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
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>
Hello, <br>
<br>
Ensembl contains domains mapped from multiple sources -
often these <br>
will <br>
be the "same" domain with slightly different
coordinates. Here you can <br>
see <br>
this on a typical transcript: <br>
<br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
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>
<br>
You should also check the overlap of your variant with
the domains, as <br>
you say using translation_start/end and
$pf->start/end. <br>
<br>
Regards <br>
<br>
Will <br>
<br>
<br>
On 14 May 2013 14:16, Guillermo Marco Puche < <br>
<a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>>
wrote: <br>
<br>
<blockquote type="cite"> Hello, <br>
<br>
This makes a lot more sense. <br>
<br>
There's something I still don't understand. For each
variation i'm <br>
getting a lot of Interpro_ac and idesc. <br>
<br>
Modified the code to debug but it stills not working
since code is <br>
trying to print undefined values. <br>
<br>
Should I compare and verify $tv->translation_start
and <br>
$tv->translation_end with $pf->start and
$pf->end to obtain the <br>
correct <br>
Interpro_ac and idesc? <br>
<br>
Thank you, <br>
<br>
Best regards. <br>
Guillermo. <br>
<br>
<br>
<br>
On 05/14/2013 02:16 PM, Will McLaren wrote: <br>
<br>
$translation->get_all_ProteinFeatures(); <br>
<br>
returns an reference to an array of ProteinFeature
objects. You'll <br>
need <br>
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 <br>
object, when actually it returns an arrayref. <br>
<br>
Regards <br>
<br>
Will <br>
<br>
<br>
On 14 May 2013 12:44, Guillermo Marco Puche < <br>
<a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>>
wrote: <br>
<br>
<blockquote type="cite"> Hello, <br>
<br>
Here's Interpro plugin code: <br>
<a moz-do-not-send="true"
class="moz-txt-link-freetext"
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 <br>
"interpro_ac" and "idesc" from my $pfeature object.
<br>
<br>
Here's a data dumper extract from $pfeature: <br>
<br>
'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' => <br>
$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>
}, <br>
<br>
ERROR: Forked process failed <br>
Plugin 'Interpro' went wrong: Can't call method
"interpro_ac" on <br>
unblessed reference at <br>
/home/likewise-open/SGNET/gmarco/.vep/Plugins/Interpro.pm
line 74 <br>
<br>
<br>
On 05/13/2013 01:49 PM, Guillermo Marco Puche wrote:
<br>
<br>
Ok I'm gonna give it a shot. <br>
I installed latest API downloaded from Ensembl
website on friday <br>
(10/05/2013) and I'm using a local Ensembl 71
database for VEP, no <br>
cache. <br>
<br>
Best regards, <br>
Guillermo <br>
<br>
On 05/13/2013 01:45 PM, Will McLaren wrote: <br>
<br>
There was a bug in --domains when using the cache
that has been <br>
recently fixed. <br>
<br>
Try updating your API and see if that's any better.
<br>
<br>
Will <br>
<br>
<br>
On 13 May 2013 12:38, Guillermo Marco Puche < <br>
<a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>>
wrote: <br>
<br>
<blockquote type="cite"> Hello Will, <br>
<br>
Yes I'm currently running VEP with --domains flag.
It always shown <br>
empty for the testings for different samples I've
done until now. <br>
So domains flag is supposed to display the
Interpro_ac for <br>
overlapping <br>
protein domains? <br>
<br>
Best regards, <br>
Guillermo. <br>
<br>
<br>
On 05/13/2013 01:34 PM, Will McLaren wrote: <br>
<br>
Hi Guillermo, <br>
<br>
Have you tried the --domains flag in the VEP? <br>
<br>
Perhaps this is not enough information for you but
it does provide <br>
the <br>
display label of overlapping protein domains. <br>
<br>
The protein object is referred to as a translation
object in the <br>
Ensembl API; you can retrieve it from the
transcript via <br>
$transcript->translation. <br>
<br>
See <br>
<a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Translation.html">http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Translation.html</a>
<br>
<br>
Regards <br>
<br>
Will <br>
<br>
<br>
On 13 May 2013 12:15, Guillermo Marco Puche < <br>
<a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>>
wrote: <br>
<br>
<blockquote type="cite"> 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 <br>
other <br>
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 <br>
interpro_ac <br>
is part from Core ProteinFeature. <br>
(EnsEMBL::ProteinFeature::interpro_ac) <br>
<br>
Best regards, <br>
Guillermo. <br>
<br>
<br>
On 05/09/2013 04:16 PM, Guillermo Marco Puche
wrote: <br>
<br>
Hello, <br>
<br>
Does anyone coded a plugin to obtain InterPro ID
and description <br>
for <br>
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>
<br>
_______________________________________________
<br>
Dev mailing list <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
<br>
Posting guidelines and subscribe/unsubscribe
info: <br>
<a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
<br>
Ensembl Blog: <a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://www.ensembl.info">http://www.ensembl.info</a>
<br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</body>
</html>