[ensembl-dev] VEP Interpro ID & description
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Fri May 17 08:22:42 BST 2013
Still waiting for someone answer before I can push it into VEP repo..
On 05/15/2013 08:43 AM, Guillermo Marco Puche wrote:
> 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.
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Dev mailing listDev at ensembl.org <mailto:Dev at ensembl.org>
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>>>>>>>
>>
>>
>> _
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