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object --+ | _paml.Paml --+ | Codeml
This class implements an interface to CODEML, part of the PAML package.
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Initialize the codeml 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. Other options found in the CODEML control have typical settings by default to run site class models 0, 1 and 2 on a nucleotide alignment.
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Dynamically build a CODEML control file from the options. The control file is written to the location specified by the ctl_file property of the codeml class.
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Parse a control file and load the options into the Codeml instance.
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Print out all of the options and their current settings.
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Convert all file/directory locations to paths relative to the current working directory. CODEML 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 codeml 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 CODEML requires relative paths.
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