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<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 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 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 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 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 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 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 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 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 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 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 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 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 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>
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<br>
<br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
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<br>
<br>
</blockquote>
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