[ensembl-dev] VEP: Plugin problems with gene adaptor

[Laurent Gil]

Hi Guillermo,

We need look into it to highlight/fix the compatibility issues of the 
VEP plugins with the new VEP.

In the meantime, you can define your own Gene adaptor in your self coded 
plugins, by inserting this code in each plugin (sorry):

use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org', # alternatively 'useastdb.ensembl.org'
-user => 'anonymous'
);
my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' ); # 
e.g. if you work on human data

$self->{ga} = $gene_adaptor; # If you want to keep using the variable 
$self->{ga}.

You can have further explanations about this code in the Ensembl API 
tutorial: http://www.ensembl.org/info/docs/api/core/core_tutorial.html

I hope this will solve your issue.
Best regards,

Laurent
Ensembl Variation

On 15/05/2017 12:06, Guillermo Marco Puche wrote:
>
> Hi Laurent,
>
> Thank you for your quick answer. I'm using gene adaptor in some self 
> coded plugins too. Do you have any quick-fix in mind or workaround?
> I'm really looking forward for this document. Will it be announced in 
> mailing list or blog? I was really scared with this big VEP update for 
> the plugin compatibility.
>
> Best regards,
> Guillermo.
>
>
> On 05/15/2017 12:17 PM, Laurent Gil wrote:
>>
>> Hi Guillermo,
>>
>> Unfortunately the VEP plugin is not compatible with the new 
>> ensembl-vep repository.
>> We need to document this plugin about this compatibility issue.
>>
>> However the new VEP (ensembl-vep) has a new option '-nearest gene' 
>> you can use with the cache:
>> http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#output
>>
>> Best regards,/
>> /
>>
>> Laurent
>> On 15/05/2017 08:44, Guillermo Marco Puche wrote:
>>>
>>> Dear devs,
>>>
>>> I've recently updated to Ensembl VEP 88 and I'm facing some problems 
>>> with some plugins. Trying to run NearestGene.pm plugin and I can't 
>>> make it run.
>>>
>>> /WARNING: Plugin 'NearestGene' went wrong: ERROR: Could not get gene 
>>> adaptor; this plugin does not work in --offline mode/
>>>
>>> There's an issue with gene adaptor code,*$self->{ga} ||= 
>>> $self->{config}->{ga}*. Trying to guess where did {ga} gone printing 
>>> Dump of $self->{config} but I can't figure this out:
>>>
>>> $VAR1 = {
>>>   'buffer_size' => 5000,
>>>   'af_1kg' => 1,
>>>   'species' => 'homo_sapiens',
>>>   'stats_html' => 1,
>>>   'host' => 'sake',
>>>   'format' => 'vcf',
>>>   'reg' => 'Bio::EnsEMBL::Registry',
>>>   'chunk_size' => 50000,
>>>   'check_existing' => 1,
>>>   'freq_pop' => '1KG_ALL',
>>>   'custom' => [],
>>>   'cell_type' => [],
>>>   'input_file' => 'test.vcf',
>>>   'tmpdir' => '/tmp',
>>>   'freq_filter' => 'exclude',
>>>   'user' => 'bioinfo',
>>>   'phastCons' => [],
>>>   'terms' => 'SO',
>>>   'delimiter' => '    ',
>>>   'dir_cache' => '/home/gmarco/.vep',
>>>   'polyphen_analysis' => 'humvar',
>>>   'cache' => 1,
>>>   'port' => '3306',
>>>   'plugin' => [
>>>     'Test'
>>>   ],
>>>   'freq_gt_lt' => 'gt',
>>>   'output_format' => 'vcf',
>>>   'phyloP' => [],
>>>   'numbers' => 1,
>>>   'af_exac' => 1,
>>>   'output_file' => '/tmp/test_88.vcf',
>>>   'database' => 0,
>>>   'freq_freq' => '0.01',
>>>   'dir_plugins' => '/home/gmarco/repositories/vep_ensembl/Plugins',
>>>   'core_type' => 'core',
>>>   'vcf' => 1,
>>>   'assembly' => 'GRCh38',
>>>   'af' => 1,
>>>   'terminal_width' => 48,
>>>   'vcf_info_field' => 'CSQ',
>>>   'transcript_filter' => [],
>>>   'af_esp' => 1,
>>>   'pick_order' => [
>>>     'canonical',
>>>     'appris',
>>>     'tsl',
>>>     'biotype',
>>>     'ccds',
>>>     'rank',
>>>     'length',
>>>     'ensembl',
>>>     'refseq'
>>>   ],
>>>   'biotype' => 1,
>>>   'cache_region_size' => 1000000,
>>>   'symbol' => 1,
>>>   'ucsc_data_root' => 'http://hgdownload.cse.ucsc.edu/goldenpath/',
>>>   'synonyms' => 
>>> '/home/gmarco/.vep/homo_sapiens/88_GRCh38/chr_synonyms.txt',
>>>   'dir' => '/home/gmarco/.vep',
>>>   'password' => 'A29bcd1234#',
>>>   'no_slice_cache' => 1,
>>>   'failed' => 0,
>>>   'force_overwrite' => 1,
>>>   'fasta' => 
>>> '/home/gmarco/.vep/homo_sapiens/88_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz'
>>> };
>>>
>>> Regards,
>>> Guillermo
>>>
>>>
>>>
>>>
>>>
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