Package Bio :: Package Phylo :: Package PAML :: Module _paml :: Class Paml
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Class Paml

source code

object --+
         |
        Paml
Known Subclasses:

Instance Methods [hide private]
 
__init__(self, alignment=None, working_dir=None, out_file=None)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
source code
 
write_ctl_file(self) source code
 
read_ctl_file(self) source code
 
print_options(self)
Print out all of the options and their current settings.
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set_options(self, **kwargs)
Set the value of an option.
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get_option(self, option)
Return the value of an option.
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get_all_options(self)
Return the values of all the options.
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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, verbose, command)
Run a paml program using the current configuration and then parse the results.
source code

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, working_dir=None, out_file=None)
(Constructor)

source code 
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

set_options(self, **kwargs)

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Set the value of an option.

This function abstracts the options dict to prevent the user from
adding options that do not exist or mispelling options.

_set_rel_paths(self)

source code 
Convert all file/directory locations to paths relative to the current working directory.

paml requires that all paths specified in the control file be
relative to the directory from which it is called rather than
absolute paths.

run(self, ctl_file, verbose, command)

source code 
Run a paml program 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 paml
requires relative paths.