[ensembl-dev] VEP Interpro ID & description

guillermo.marco at sistemasgenomicos.com guillermo.marco at sistemasgenomicos.com
Sat Jun 8 09:06:22 BST 2013


I've been trying that but I don't know exactly where to use =~ /\Q$result\E.
I'm confused.

I suppose when I save var $idesc

> 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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