[ensembl-dev] VEP Interpro ID & description
Laurent Gil
lgil at ebi.ac.uk
Mon Jun 10 10:47:09 BST 2013
Hi Guillermo,
I think Sarah was alking about the line 115 of your plugin:
elsif ($interpro_data[0] =~ /$interpro_ac/ || $interpro_data[1] =~ /$idesc/) {
Where you need to replace the code "$interpro_data[1] =~/$idesc/" by
"$interpro_data[1] =~ /\Q$idesc\E/"
Cheers,
Laurent
On 08/06/2013 09:06, guillermo.marco at sistemasgenomicos.com wrote:
> 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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