[ensembl-dev] VEP Interpro ID & description

Guillermo Marco Puche guillermo.marco at sistemasgenomicos.com
Fri Jun 7 07:23:04 BST 2013


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 
>> <mailto: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
>>>>>     <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>
>>>>>>>>>>                     Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>>>>                     Ensembl Blog:http://www.ensembl.info  <http://www.ensembl.info/>
>>>>>>>>>
>>>>
>>     ------------------------------------------------------------------------
>>
>
>
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