[ensembl-dev] VEP Interpro ID & description
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Fri Jun 7 07:23:04 BST 2013
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
>> <mailto: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
>>>>> <mailto: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
>>>>>> <mailto: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
>>>>>>>> <mailto: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
>>>>>>>>> <mailto: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 listDev at ensembl.org <mailto:Dev at ensembl.org>
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>>>>>>>>>
>>>>
>> ------------------------------------------------------------------------
>>
>
>
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