[ensembl-dev] VEP Interpro ID & description
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Tue May 14 17:15:33 BST 2013
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
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>>>>>
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