<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>
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.<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>
This seems wrong coding error with regex but there's no regex on
that line: <br>
<br>
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
<span class="k" style="margin: 0px; padding: 0px; border: 0px;
font-weight: bold; color: rgb(51, 51, 51); font-family:
Consolas, 'Liberation Mono', Courier, monospace; font-size:
12px; font-style: normal; font-variant: normal; letter-spacing:
normal; line-height: 18px; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: pre;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">if</span><span
style="color: rgb(51, 51, 51); font-family: Consolas,
'Liberation Mono', Courier, monospace; font-size: 12px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: 18px; orphans: auto;
text-align: start; text-indent: 0px; text-transform: none;
white-space: pre; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); display: inline !important; float: none;"> </span><span
class="p" style="margin: 0px; padding: 0px; border: 0px; color:
rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono',
Courier, monospace; font-size: 12px; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: 18px; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: pre;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">(</span><span class="o"
style="margin: 0px; padding: 0px; border: 0px; font-weight:
bold; color: rgb(51, 51, 51); font-family: Consolas, 'Liberation
Mono', Courier, monospace; font-size: 12px; font-style: normal;
font-variant: normal; letter-spacing: normal; line-height: 18px;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: pre; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">!</span><span class="nv"
style="margin: 0px; padding: 0px; border: 0px; color: rgb(0,
128, 128); font-family: Consolas, 'Liberation Mono', Courier,
monospace; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal;
line-height: 18px; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: pre;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">$interpro_data</span><span
class="p" style="margin: 0px; padding: 0px; border: 0px; color:
rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono',
Courier, monospace; font-size: 12px; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: 18px; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: pre;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">[</span><span class="mi"
style="margin: 0px; padding: 0px; border: 0px; color: rgb(0,
153, 153); font-family: Consolas, 'Liberation Mono', Courier,
monospace; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal;
line-height: 18px; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: pre;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">0</span><span class="p"
style="margin: 0px; padding: 0px; border: 0px; color: rgb(51,
51, 51); font-family: Consolas, 'Liberation Mono', Courier,
monospace; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal;
line-height: 18px; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: pre;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">]</span><span
style="color: rgb(51, 51, 51); font-family: Consolas,
'Liberation Mono', Courier, monospace; font-size: 12px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: 18px; orphans: auto;
text-align: start; text-indent: 0px; text-transform: none;
white-space: pre; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); display: inline !important; float: none;"> </span><span
class="o" style="margin: 0px; padding: 0px; border: 0px;
font-weight: bold; color: rgb(51, 51, 51); font-family:
Consolas, 'Liberation Mono', Courier, monospace; font-size:
12px; font-style: normal; font-variant: normal; letter-spacing:
normal; line-height: 18px; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: pre;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">&&</span><span
style="color: rgb(51, 51, 51); font-family: Consolas,
'Liberation Mono', Courier, monospace; font-size: 12px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: 18px; orphans: auto;
text-align: start; text-indent: 0px; text-transform: none;
white-space: pre; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); display: inline !important; float: none;"> </span><span
class="o" style="margin: 0px; padding: 0px; border: 0px;
font-weight: bold; color: rgb(51, 51, 51); font-family:
Consolas, 'Liberation Mono', Courier, monospace; font-size:
12px; font-style: normal; font-variant: normal; letter-spacing:
normal; line-height: 18px; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: pre;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">!</span><span class="nv"
style="margin: 0px; padding: 0px; border: 0px; color: rgb(0,
128, 128); font-family: Consolas, 'Liberation Mono', Courier,
monospace; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal;
line-height: 18px; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: pre;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">$interpro_data</span><span
class="p" style="margin: 0px; padding: 0px; border: 0px; color:
rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono',
Courier, monospace; font-size: 12px; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: 18px; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: pre;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">[</span><span class="mi"
style="margin: 0px; padding: 0px; border: 0px; color: rgb(0,
153, 153); font-family: Consolas, 'Liberation Mono', Courier,
monospace; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal;
line-height: 18px; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: pre;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">1</span><span class="p"
style="margin: 0px; padding: 0px; border: 0px; color: rgb(51,
51, 51); font-family: Consolas, 'Liberation Mono', Courier,
monospace; font-size: 12px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal;
line-height: 18px; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: pre;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">])</span><span
style="color: rgb(51, 51, 51); font-family: Consolas,
'Liberation Mono', Courier, monospace; font-size: 12px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: 18px; orphans: auto;
text-align: start; text-indent: 0px; text-transform: none;
white-space: pre; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); display: inline !important; float: none;"> </span><br>
<br>
Guille.<br>
<br>
On 05/17/2013 10:17 AM, Guillermo Marco Puche wrote:<br>
</div>
<blockquote cite="mid:5195E782.2010306@sistemasgenomicos.com"
type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<div class="moz-cite-prefix">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
cite="mid:CAMVEDX0=bmkE68z-_OYEOzOXA4RVFBu37xX8FhbvezfJPF5LcQ@mail.gmail.com"
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 style="">Cheers</div>
<div style=""><br>
</div>
<div style="">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 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>Still waiting for someone answer before I can push
it into VEP repo..
<div>
<div class="h5"><br>
<br>
On 05/15/2013 08:43 AM, Guillermo Marco Puche
wrote:<br>
</div>
</div>
</div>
<div>
<div class="h5">
<blockquote type="cite">
<div>Hello,<br>
<br>
Fixed a bug in script about empty Interpro_ac
and idesc. <br>
Git code updated: <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>
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
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>
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 moz-do-not-send="true"
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 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 $pf->end to
obtain the correct Interpro_ac and
idesc?<br>
<br>
Thank you,<br>
<br>
Best regards.<span><font
color="#888888"><br>
Guillermo.</font></span>
<div>
<div><br>
<br>
<br>
On 05/14/2013 02:16 PM, Will
McLaren wrote:<br>
</div>
</div>
</div>
<div>
<div>
<blockquote type="cite">
<div dir="ltr">$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
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>
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