[ensembl-dev] VEP Interpro ID & description
Sarah Hunt
seh at ebi.ac.uk
Fri Jun 7 12:18:50 BST 2013
Hi Guillermo,
If you paste the string from the error message into the interpro search you
will get the result '(+) RNA virus helicase core domain (IPR027351)'. The
'+' in the string will be interpreted as a special character unless you
escape it.
Try something like =~ /\Q$result\E/
Best wishes,
Sarah
On Fri, Jun 7, 2013 at 7:23 AM, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:
> Hello,
>
> Using my InterPro plugin I got this error i've never seen before:
>
> Plugin 'Interpro' went wrong: Quantifier follows nothing in regex; marked
> by <-- HERE in m/(+ <-- HERE )RNA_virus_helicase_core_dom/ at
> ./vep_config/Plugins/Interpro.pm line 112.
>
>
> Here's Interpro plugin code:
> https://github.com/guillermomarco/vep_plugins_71/blob/master/Interpro.pm
>
> This seems wrong coding error with regex but there's no regex on that
> line:
>
> if (!$interpro_data[0] && !$interpro_data[1])
>
> Guille.
>
>
> On 05/17/2013 10:17 AM, Guillermo Marco Puche wrote:
>
> Hello Will,
>
> That's seem very logic. But even if I advertise on my plugin I would like
> to hear the opinion from other devs.
> I don't want people to use a plugin that isn't working properly or giving
> wrong information.
>
> Thank you.
>
> Best regards,
> Guillermo.
>
> On 05/17/2013 10:10 AM, Will McLaren wrote:
>
> Hi Guillermo,
>
> We're currently working on getting some official guidelines for external
> submissions of code in place.
>
> Until that happens, we can't put plugins in the Ensembl VEP_plugins repo.
> However, feel free to advertise your plugins on your own GitHub, as you
> have done here!
>
> Cheers
>
> Will
>
>
> On 17 May 2013 08:22, Guillermo Marco Puche <
> guillermo.marco at sistemasgenomicos.com> wrote:
>
>> 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> 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.
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Dev mailing list Dev at ensembl.org
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>>>>>>
>>>>>>
>> ------------------------------
>>
>
>
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