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.

Only the input and out parameters are mandatory.

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

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

References

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. https://doi.org/10.1371/journal.pone.0009490.

Examples

>>> import _Fasttree
>>> fasttree_exe = r"C:\FasttreeWin32\fasttree.exe"
>>> cmd = _Fasttree.FastTreeCommandline(fasttree_exe,
...                                     input=r'C:\Input\ExampleAlignment.fsa',
...                                     out=r'C:\Output\ExampleTree.tree')
>>> print(cmd)
>>> out, err = cmd()
>>> print(out)
>>> print(err)
Instance Methods [hide private]
 
__init__(self, cmd='fasttree', **kwargs)
Initialize the class.
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__

Class Variables [hide private]

Inherited from Application.AbstractCommandline: parameters

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

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

source code 
Initialize the class.
Overrides: object.__init__