[ensembl-dev] VEP Interpro ID & description
Will McLaren
wm2 at ebi.ac.uk
Fri May 17 09:10:13 BST 2013
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.
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>> Ensembl Blog: http://www.ensembl.info
>>>>>
>>>>>
>
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