[ensembl-dev] VEP Interpro ID & description

[Guillermo Marco Puche]

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/
>>>
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