Method: Bio::PAML::Common#run

Defined in:
lib/bio/appl/paml/common.rb

#run(control_file) ⇒ Object

Runs the program on the parameters in the passed control file. No parameters checks are performed. All internal parameters are ignored and are kept untouched. The output and report attributes are cleared in this method.

Warning about PAML’s behavior: PAML writes supplemental output files in the current directory with fixed file names which can not be changed with parameters or command-line options, for example, rates, rst, and rub. This behavior may ovarwrite existing files, especially previous supplemental results.

Arguments:

  • (optional) control_file: file name of control file (String)

Returns

messages printed to the standard output (String)



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# File 'lib/bio/appl/paml/common.rb', line 95

def run(control_file)
  exec_local([ control_file ])
end