[ensembl-dev] VEP Interpro ID & description
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Fri May 17 09:17:06 BST 2013
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>
>>>>>>>>> Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>>> Ensembl Blog:http://www.ensembl.info <http://www.ensembl.info/>
>>>>>>>>
>>>
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