[ensembl-dev] minor errors in VEP?

[Andrea Edwards]

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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