[ensembl-dev] VEP Interpro ID & description
Will McLaren
wm2 at ebi.ac.uk
Tue May 14 14:38:17 BST 2013
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> 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> 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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