[ensembl-dev] minor errors in VEP?

[Andrea Edwards]

You're welcome! Thanks for writing it :-)

On 05/05/11 13:45, Will McLaren wrote:
> 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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>>