[ensembl-dev] VEP FATHMM plugin

[Michael Yourshaw]

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;

ॐ

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.





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.
> 
> 
> 
> ॐ
> 
> 
> 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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