[ensembl-dev] VEP FATHMM plugin

Will McLaren wm2 at ebi.ac.uk
Thu Nov 14 11:34:00 GMT 2013


Thanks again Michael, fixed.

Will


On 14 November 2013 02:24, Michael Yourshaw <myourshaw at ucla.edu> wrote:

> Thanks for the quick response, Will.
>
> Now there is a different issue. The quotes get passed through to the
> plugin.
>
> For example, in FATHMM, the $self->{command} is
>
> "python /share/apps/myourshaw/VEP_plugins/fathmm/fathmm.py”
>
> rather than
>
> python /share/apps/myourshaw/VEP_plugins/fathmm/fathmm.py
>
> The plugin throws an exception when it tries to run the command parameter
> (surrounded by quotes) in the shell in the line
>
> my $fathmm_err = `cd $command_dir; $command $tmp_in_file $tmp_out_file;`;
>
> I think what’s needed in VEP is to change this line
>         # remove quotes
>         s/[\"\']//g;
> to
>         # remove quotes
>         s/[\"\']//g for @split;
>
>>
> Michael Yourshaw
> UCLA Geffen School of Medicine
> Department of Human Genetics, Nelson Lab
> 695 Charles E Young Drive S
> Gonda 5554
>
> Los Angeles CA 90095-8348 USA
>
> myourshaw at ucla.edu
>
> 970.691.8299
>
> This message is intended only for the use of the addressee and may contain
> information that is PRIVILEGED and CONFIDENTIAL, and/or may contain
> ATTORNEY WORK PRODUCT. If you are not the intended recipient, you are
> hereby notified that any dissemination of this communication is strictly
> prohibited. If you have received this communication in error, please erase
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> Thank you.
>
>
>
>
> On Nov 13, 2013, at 00:52, Will McLaren <wm2 at ebi.ac.uk> wrote:
>
> Hi Michael,
>
> Thanks for finding this; I've committed a fix to the CVS (branch 73).
>
> It should work now if you use quotes - it won't work if you don't have
> quotes due to the way the config parser has to work.
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
>
> On 13 November 2013 02:43, Michael Yourshaw <myourshaw at ucla.edu> wrote:
>
>> I’m having a problem with the FATHMM plugin parameters. I think this will
>> affect all plugins that need a space in the text when the plugin is
>> specified in a configuration file.
>>
>> The plugin wants to be specified like this:
>> FATHMM,"python /path/to/fathmm/fathmm.py”
>>
>> I am using a configuration file with parameters in that form, but the
>> VEP read_config_from_file subroutine seems to be splitting on the space
>> between ‘python’ and ‘/path/to’. This happens whether I use the enclosing
>> double quotes or not.
>>
>> The space in a plugin parameter isn’t a problem on the command line, just
>> in a config file.
>>
>>
>>
>>>>
>> Michael Yourshaw
>> UCLA Geffen School of Medicine
>> Department of Human Genetics, Nelson Lab
>> 695 Charles E Young Drive S
>> Gonda 5554
>>
>> Los Angeles CA 90095-8348 USA
>>
>> myourshaw at ucla.edu
>>
>> 970.691.8299
>>
>> This message is intended only for the use of the addressee and may
>> contain information that is PRIVILEGED and CONFIDENTIAL, and/or may contain
>> ATTORNEY WORK PRODUCT. If you are not the intended recipient, you are
>> hereby notified that any dissemination of this communication is strictly
>> prohibited. If you have received this communication in error, please erase
>> all copies of the message and its attachments and notify us immediately.
>> Thank you.
>>
>>
>>
>>
>>
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