[ensembl-dev] VEP FATHMM plugin

Michael Yourshaw myourshaw at ucla.edu
Wed Nov 13 02:43:50 GMT 2013


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

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