[ensembl-dev] VEP Interpro ID & description
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Mon Jun 10 12:02:44 BST 2013
Heelo Laurent,
I'll try and report back.
Thank you very much.
Best regards,
Guillermo.
On 06/10/2013 11:47 AM, Laurent Gil wrote:
> Hi Guillermo,
>
> I think Sarah was alking about the line 115 of your plugin:
>
> elsif ($interpro_data[0] =~ /$interpro_ac/ || $interpro_data[1]
> =~ /$idesc/) {
>
> Where you need to replace the code "$interpro_data[1] =~/$idesc/" by
> "$interpro_data[1] =~ /\Q$idesc\E/"
>
>
> Cheers,
>
> Laurent
>
> On 08/06/2013 09:06, guillermo.marco at sistemasgenomicos.com wrote:
>> I've been trying that but I don't know exactly where to use =~
>> /\Q$result\E.
>> I'm confused.
>>
>> I suppose when I save var $idesc
>>
>>> Hi Guillermo,
>>>
>>> If you paste the string from the error message into the interpro search
>>> you
>>> will get the result '(+) RNA virus helicase core domain
>>> (IPR027351)'. The
>>> '+' in the string will be interpreted as a special character unless you
>>> escape it.
>>>
>>> Try something like =~ /\Q$result\E/
>>> Best wishes,
>>>
>>> Sarah
>>> On Fri, Jun 7, 2013 at 7:23 AM, Guillermo Marco Puche <
>>> guillermo.marco at sistemasgenomicos.com> wrote:
>>>
>>>> Hello,
>>>>
>>>> Using my InterPro plugin I got this error i've never seen before:
>>>>
>>>> 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.
>>>>
>>>>
>>>> Here's Interpro plugin code:
>>>> https://github.com/guillermomarco/vep_plugins_71/blob/master/Interpro.pm
>>>>
>>>>
>>>> This seems wrong coding error with regex but there's no regex on that
>>>> line:
>>>>
>>>> if (!$interpro_data[0] && !$interpro_data[1])
>>>>
>>>> Guille.
>>>>
>>>>
>>>> On 05/17/2013 10:17 AM, Guillermo Marco Puche wrote:
>>>>
>>>> Hello Will,
>>>>
>>>> That's seem very logic. But even if I advertise on my plugin I would
>>>> like
>>>> to hear the opinion from other devs.
>>>> I don't want people to use a plugin that isn't working properly or
>>>> giving
>>>> wrong information.
>>>>
>>>> Thank you.
>>>>
>>>> Best regards,
>>>> Guillermo.
>>>>
>>>> On 05/17/2013 10:10 AM, Will McLaren wrote:
>>>>
>>>> Hi Guillermo,
>>>>
>>>> We're currently working on getting some official guidelines for
>>>> external
>>>> submissions of code in place.
>>>>
>>>> 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!
>>>>
>>>> Cheers
>>>>
>>>> Will
>>>>
>>>>
>>>> On 17 May 2013 08:22, Guillermo Marco Puche <
>>>> guillermo.marco at sistemasgenomicos.com> wrote:
>>>>
>>>>> Still waiting for someone answer before I can push it into VEP
>>>>> repo..
>>>>>
>>>>>
>>>>> On 05/15/2013 08:43 AM, Guillermo Marco Puche wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> Fixed a bug in script about empty Interpro_ac and idesc.
>>>>> Git code updated:
>>>>> https://github.com/guillermomarco/vep_plugins_71/blob/master/Interpro.pm
>>>>>
>>>>>
>>>>> If someone give me the OK I'll push it to official VEP-plugin
>>>>> repository.
>>>>>
>>>>> Best regards,
>>>>> Guillermo.
>>>>>
>>>>> On 05/14/2013 06:15 PM, Guillermo Marco Puche wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> I've come to this plugin:
>>>>> https://github.com/guillermomarco/vep_plugins_71/blob/master/Interpro.pm
>>>>>
>>>>>
>>>>> If you could check code and test it would be awesome !
>>>>>
>>>>> I'm not 100% sure it's working perfectly.
>>>>>
>>>>> Thank you.
>>>>>
>>>>> Best regards,
>>>>> Guillermo.
>>>>>
>>>>> On 05/14/2013 03:38 PM, Will McLaren wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> 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:
>>>>>
>>>>>
>>>>> http://www.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000128573;r=7:114055052-114333823;t=ENST00000403559
>>>>>
>>>>>
>>>>> You should also check the overlap of your variant with the
>>>>> domains, as
>>>>> you say using translation_start/end and $pf->start/end.
>>>>>
>>>>> Regards
>>>>>
>>>>> Will
>>>>>
>>>>>
>>>>> On 14 May 2013 14:16, Guillermo Marco Puche <
>>>>> guillermo.marco at sistemasgenomicos.com> wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> This makes a lot more sense.
>>>>>>
>>>>>> There's something I still don't understand. For each variation i'm
>>>>>> getting a lot of Interpro_ac and idesc.
>>>>>>
>>>>>> Modified the code to debug but it stills not working since code is
>>>>>> trying to print undefined values.
>>>>>>
>>>>>> 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?
>>>>>>
>>>>>> Thank you,
>>>>>>
>>>>>> Best regards.
>>>>>> Guillermo.
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 05/14/2013 02:16 PM, Will McLaren wrote:
>>>>>>
>>>>>> $translation->get_all_ProteinFeatures();
>>>>>>
>>>>>> returns an reference to an array of ProteinFeature objects. You'll
>>>>>> need
>>>>>> to iterate over them something like:
>>>>>>
>>>>>> foreach my $pf(@{$translation->get_all_ProteinFeatures}) {
>>>>>> $interpro{"INTERPRO_AC"} = $pf-> interpro_ac;
>>>>>> etc...
>>>>>> }
>>>>>>
>>>>>> There is a mistake in the method docs that says it returns a single
>>>>>> object, when actually it returns an arrayref.
>>>>>>
>>>>>> Regards
>>>>>>
>>>>>> Will
>>>>>>
>>>>>>
>>>>>> On 14 May 2013 12:44, Guillermo Marco Puche <
>>>>>> guillermo.marco at sistemasgenomicos.com> wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> Here's Interpro plugin code:
>>>>>>> https://github.com/guillermomarco/vep_plugins_71/blob/master/Interpro.pm
>>>>>>>
>>>>>>>
>>>>>>> I'm getting unblessed reference error when trying to extract
>>>>>>> "interpro_ac" and "idesc" from my $pfeature object.
>>>>>>>
>>>>>>> Here's a data dumper extract from $pfeature:
>>>>>>>
>>>>>>> 'Bio::EnsEMBL::ProteinFeature' ),
>>>>>>> bless( {
>>>>>>> 'p_value' => '1.6e-42',
>>>>>>> 'coverage' => undef,
>>>>>>> 'percent_id' => '0',
>>>>>>> 'adaptor' => $VAR1->[0]{'adaptor'},
>>>>>>> 'hstrand' => undef,
>>>>>>> 'idesc' => 'DH-domain',
>>>>>>> 'hdescription' => undef,
>>>>>>> 'slice' => undef,
>>>>>>> 'dbname' => undef,
>>>>>>> 'hspecies' => undef,
>>>>>>> 'dbID' => '6415086',
>>>>>>> 'strand' => 0,
>>>>>>> 'seqname' => '936060',
>>>>>>> 'translation_id' => '',
>>>>>>> 'external_db_id' => undef,
>>>>>>> 'db_display_name' => undef,
>>>>>>> 'hend' => 0,
>>>>>>> 'hcoverage' => undef,
>>>>>>> 'score' => '0',
>>>>>>> 'species' => undef,
>>>>>>> 'interpro_ac' => 'IPR000219',
>>>>>>> 'end' => 985,
>>>>>>> 'analysis' =>
>>>>>>> $VAR1->[0]{'analysis'}{'adaptor'}{'_logic_name_cache'}{'superfamily'},
>>>>>>>
>>>>>>> 'hseqname' => 'SSF48065',
>>>>>>> 'hstart' => 0,
>>>>>>> 'extra_data' => undef,
>>>>>>> 'group_id' => undef,
>>>>>>> 'level_id' => undef,
>>>>>>> 'start' => 803
>>>>>>> },
>>>>>>>
>>>>>>> ERROR: Forked process failed
>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>> On 05/13/2013 01:49 PM, Guillermo Marco Puche wrote:
>>>>>>>
>>>>>>> Ok I'm gonna give it a shot.
>>>>>>> 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.
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Guillermo
>>>>>>>
>>>>>>> On 05/13/2013 01:45 PM, Will McLaren wrote:
>>>>>>>
>>>>>>> There was a bug in --domains when using the cache that has been
>>>>>>> recently fixed.
>>>>>>>
>>>>>>> Try updating your API and see if that's any better.
>>>>>>>
>>>>>>> Will
>>>>>>>
>>>>>>>
>>>>>>> On 13 May 2013 12:38, Guillermo Marco Puche <
>>>>>>> guillermo.marco at sistemasgenomicos.com> wrote:
>>>>>>>
>>>>>>>> Hello Will,
>>>>>>>>
>>>>>>>> Yes I'm currently running VEP with --domains flag. It always shown
>>>>>>>> empty for the testings for different samples I've done until now.
>>>>>>>> So domains flag is supposed to display the Interpro_ac for
>>>>>>>> overlapping
>>>>>>>> protein domains?
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>> Guillermo.
>>>>>>>>
>>>>>>>>
>>>>>>>> On 05/13/2013 01:34 PM, Will McLaren wrote:
>>>>>>>>
>>>>>>>> Hi Guillermo,
>>>>>>>>
>>>>>>>> Have you tried the --domains flag in the VEP?
>>>>>>>>
>>>>>>>> Perhaps this is not enough information for you but it does provide
>>>>>>>> the
>>>>>>>> display label of overlapping protein domains.
>>>>>>>>
>>>>>>>> The protein object is referred to as a translation object in the
>>>>>>>> Ensembl API; you can retrieve it from the transcript via
>>>>>>>> $transcript->translation.
>>>>>>>>
>>>>>>>> See
>>>>>>>> http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Translation.html
>>>>>>>>
>>>>>>>>
>>>>>>>> Regards
>>>>>>>>
>>>>>>>> Will
>>>>>>>>
>>>>>>>>
>>>>>>>> On 13 May 2013 12:15, Guillermo Marco Puche <
>>>>>>>> guillermo.marco at sistemasgenomicos.com> wrote:
>>>>>>>>
>>>>>>>>> Hello,
>>>>>>>>>
>>>>>>>>> So it seems nobody has done this yet. I'll do it then :)
>>>>>>>>>
>>>>>>>>> Does VEP support any kind of """Proteinfeature"""? Checking the
>>>>>>>>> other
>>>>>>>>> scripts it seems I must be using Transcript feature_type.
>>>>>>>>>
>>>>>>>>> Correct me if I'm wrong please, I'm a bit confused since
>>>>>>>>> interpro_ac
>>>>>>>>> is part from Core ProteinFeature.
>>>>>>>>> (EnsEMBL::ProteinFeature::interpro_ac)
>>>>>>>>>
>>>>>>>>> Best regards,
>>>>>>>>> Guillermo.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 05/09/2013 04:16 PM, Guillermo Marco Puche wrote:
>>>>>>>>>
>>>>>>>>> Hello,
>>>>>>>>>
>>>>>>>>> Does anyone coded a plugin to obtain InterPro ID and description
>>>>>>>>> for
>>>>>>>>> VEP?
>>>>>>>>> I've looked in VEP repo without luck.
>>>>>>>>>
>>>>>>>>> I want to know before start coding.
>>>>>>>>>
>>>>>>>>> Thank you !
>>>>>>>>>
>>>>>>>>> Best regards,
>>>>>>>>> Guillermo.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Dev mailing list Dev at ensembl.org
>>>>>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>>> Ensembl Blog: http://www.ensembl.info
>>>>>>>>>
>>>>>>>>>
>>>>> ------------------------------
>>>>>
>>>>
>>>> _______________________________________________
>>>> Dev mailing list Dev at ensembl.org
>>>> Posting guidelines and subscribe/unsubscribe info:
>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>
>>>> Ensembl Blog: http://www.ensembl.info/
>>>>
>>>>
>>>> _______________________________________________
>>>> Dev mailing list Dev at ensembl.org
>>>> Posting guidelines and subscribe/unsubscribe info:
>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>> Ensembl Blog: http://www.ensembl.info/
>>>>
>>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20130610/6c1d1aa4/attachment.html>
More information about the Dev
mailing list