Command Line Interface

User guide

The command line interface has built in help. To display the help, please append -h to the program call, for example:

./patapy.py -h

The help option responds to arguments your provide, so you can get details about your method of choice with:

./patapy.py gsea -h

where gsea is the name of a method; likewise, you can display help for any of samples specification options (case/control/data), e.g.:

./patapy.py control -h

Predefined parsers

Parsers are defined in command_line.main module.

Creating custom arguments and parsers

Please see declarative_parser module documentation for instructions.