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

Class Paml

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.

source code

set_options(self, **kwargs)
Set the value of an option.

source code

get_option(self, option)
Return the value of an option.

source code

get_all_options(self)
Return the values of all the options.

source code

_set_rel_paths(self)
Convert all file/directory locations to paths relative to the current working directory.

source code

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__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

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)

source code

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.

Class Paml

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

set_options(self, **kwargs)

_set_rel_paths(self)

run(self, ctl_file, verbose, command)

init(self, alignment=None, working_dir=None, out_file=None)
(Constructor)