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

[Will McLaren]

Hi Guillermo,

Another user contributed a pull request which should fix this issue for you:

https://github.com/Ensembl/VEP_plugins/commit/7c865b4898540bff2d9acfb68f4e9ac513c9e74a

Cheers

Will McLaren
Ensembl Variation

On 15 May 2017 at 15:51, Laurent Gil <lgil at ebi.ac.uk> wrote:

> 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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