[ensembl-dev] minor errors in VEP?

[Will McLaren]

Thanks for spotting these Andrea

Will

On 5 May 2011 13:29, Andrea Edwards <edwardsa at cs.man.ac.uk> wrote:
> Hi
>
> Sorry to be a pain but I have found a couple of very minor errors in the VEP
> script.
>
> In the readme file it says to use --registry_file as the flag whereas in the
> code you are loading $config->{registry}
> Naturally all you have to do to fix this is to change the flag in the config
> file to --registry but it might save other people the time finding the
> problem. I spotted this when i found it was taking this long to run the
> script (i thought 7 minutes to run 20 variants was extremely slow so I
> guessed i was using the external database but even in the old script you can
> do 100 annotations a minute against the external db????)
>
> workspace/snp$ variant_effect_predictor.pl --config config.txt
> #----------------------------------#
> # ENSEMBL VARIANT EFFECT PREDICTOR #
> #----------------------------------#
>
> version 2.0
>
> By Will McLaren (wm2 at ebi.ac.uk)
>
> Configuration options:
>
> config           config.txt
> input_file       input.vep
> output_file      vep_output.txt
> registry_file    registry.txt
> species          homo_sapiens
> terms            display
> verbose
>
> --------------------
>
> 2011-05-05 12:26:33 - Starting...
> 2011-05-05 12:28:48 - Processed 10 variants
> 2011-05-05 12:33:36 - Processed 20 variants
>
>
> But this is back to normal speed when i changed the config file to
> --registry.
>
> There is another small error after that. See the output
>
> Configuration options:
>
> config         config.txt
> input_file     input.vep
> output_file    vep_output.txt
> registry       registry.txt
> species        homo_sapiens
> terms          display
> verbose
>
> --------------------
>
> 2011-05-05 13:01:21 - Loading DB config from registry file registry.txt
> 2011-05-05 13:01:21 - Starting...
> 2011-05-05 13:01:24 - Processed 10 variants
> 2011-05-05 13:01:27 - Processed 20 variants
> 2011-05-05 13:01:34 - Processed 30 variants
>
>
>  note i am running in verbose mode and this code never runs
>
>     if($config->{verbose}) {
>
>         # get a meta container adaptors to check version
>         my $core_mca = $reg->get_adaptor($config->{species}, 'core',
> 'metacontainer');
>         my $var_mca = $reg->get_adaptor($config->{species}, 'variation',
> 'metacontainer');
>
>         if($core_mca && $var_mca) {
>             debug(
>                 "Connected to core version ", $core_mca->get_schema_version,
> " database ",
>                 "and variation version ", $var_mca->get_schema_version, "
> database"
>             );
>         }
>     }
>
>
> This is because $config->verbose = '' so i changed it to
> if(defined($config->{verbose}))  to get the output
>
> cheers
>
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