[ensembl-dev] VEP Interpro ID & description
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Tue May 14 14:16:23 BST 2013
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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