[ensembl-dev] VEP Interpro ID & description
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Wed May 15 07:43:11 BST 2013
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.
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>
>
>
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