[ensembl-dev] VEP Interpro ID & description

[Will McLaren]

$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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