Package Bio :: Package Phylo :: Package PAML :: Module yn00 :: Class Yn00
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Class Yn00

source code

object --+    
         |    
_paml.Paml --+
             |
            Yn00

This class implements an interface to yn00, part of the PAML package.

Instance Methods [hide private]
 
__init__(self, alignment=None, working_dir=None, out_file=None)
Initialize the Yn00 instance.
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write_ctl_file(self)
Dynamically build a yn00 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 yn00 instance.
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run(self, ctl_file=None, verbose=False, command='yn00', parse=True)
Run a paml program 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 _paml.Paml (private): _set_rel_paths

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 
Initialize the Yn00 instance.

The user may optionally pass in strings specifying the locations
of the input alignment, the working directory and
the final output file.

Overrides: object.__init__

write_ctl_file(self)

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Dynamically build a yn00 control file from the options.

The control file is written to the location specified by the
ctl_file property of the yn00 class.

Overrides: _paml.Paml.write_ctl_file

read_ctl_file(self, ctl_file)

source code 
Parse a control file and load the options into the yn00 instance.
        

Overrides: _paml.Paml.read_ctl_file

run(self, ctl_file=None, verbose=False, command='yn00', parse=True)

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.

Overrides: _paml.Paml.run
(inherited documentation)