Package Bio :: Package Phylo :: Package Applications :: Module _Fasttree :: Class FastTreeCommandline
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Class FastTreeCommandline

source code

                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 FastTreeCommandline

Command-line wrapper for FastTree.

Homepage: http://www.microbesonline.org/fasttree/

Citations:

Price, M.N., Dehal, P.S., and Arkin, A.P. (2010) FastTree 2 -- Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, 5(3):e9490. doi:10.1371/journal.pone.0009490.

Example usage:

>>> import _Fasttree
>>> fasttree_exe = r"C:\FasttreeWin32 asttree.exe"
>>> cmd = _Fasttree.FastTreeCommandline(fasttree_exe, input=r'C:\Input\ExampleAlignment.fsa', out='C:\Output\ExampleTree.tree')
>>> print(cmd)
>>> out, err = cmd()
>>> print(out)
>>> print(err)

Usage advice: the only parameters needed are (fasttree_exe, input='<InputFile>' out='<OutputFile>')

parameters that use values are added this way: (fasttree_exe, parameter=value, input='<InputFile>' out='<OutputFile>') parameters that don't use values are added this way: (fasttree_exe, parameter=True, input='<InputFile>' out='<OutputFile>')

from the command line use 'fasttree.exe -help' or 'fasttree.exe -expert' for more explanation of usage options

Instance Methods [hide private]
 
__init__(self, cmd='fasttree', **kwargs)
Create a new instance of a command line wrapper object.
source code

Inherited from Application.AbstractCommandline: __call__, __repr__, __setattr__, __str__, set_parameter

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

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, cmd='fasttree', **kwargs)
(Constructor)

source code 
Create a new instance of a command line wrapper object.
Overrides: object.__init__
(inherited documentation)