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object --+ | _paml.Paml --+ | Baseml
This class implements an interface to BASEML, part of the PAML package.
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Initialize the Baseml instance. The user may optionally pass in strings specifying the locations of the input alignment and tree files, the working directory and the final output file.
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Dynamically build a BASEML control file from the options. The control file is written to the location specified by the ctl_file property of the baseml class.
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Parse a control file and load the options into the Baseml instance.
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Convert all file/directory locations to paths relative to the current working directory. BASEML requires that all paths specified in the control file be relative to the directory from which it is called rather than absolute paths.
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Run baseml using the current configuration and then parse the results. Return a process signal so the user can determine if the execution was successful (return code 0 is successful, -N indicates a failure). The arguments may be passed as either absolute or relative paths, despite the fact that BASEML requires relative paths.
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