Package Bio :: Package Phylo :: Package PAML :: Module baseml :: Class Baseml
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Class Baseml

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object --+    
         |    
_paml.Paml --+
             |
            Baseml

This class implements an interface to BASEML, part of the PAML package.

Instance Methods [hide private]
 
__init__(self, alignment=None, tree=None, working_dir=None, out_file=None)
Initialize the Baseml instance.
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write_ctl_file(self)
Dynamically build a BASEML control file from the options.
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read_ctl_file(self, ctl_file)
Parse a control file and load the options into the Baseml instance.
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_set_rel_paths(self)
Convert all file/directory locations to paths relative to the current working directory.
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run(self, ctl_file=None, verbose=False, command='baseml', parse=True)
Run baseml using the current configuration and then parse the results.
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Inherited from _paml.Paml: get_all_options, get_option, print_options, set_options

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, alignment=None, tree=None, working_dir=None, out_file=None)
(Constructor)

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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.

Overrides: object.__init__

write_ctl_file(self)

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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.

Overrides: _paml.Paml.write_ctl_file

read_ctl_file(self, ctl_file)

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Parse a control file and load the options into the Baseml instance.
        

Overrides: _paml.Paml.read_ctl_file

_set_rel_paths(self)

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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.

Overrides: _paml.Paml._set_rel_paths

run(self, ctl_file=None, verbose=False, command='baseml', parse=True)

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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.

Overrides: _paml.Paml.run