[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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