Package Bio :: Package Align :: Package Applications :: Module _Clustalw :: Class ClustalwCommandline
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Class ClustalwCommandline

source code

                     object --+    
Application.AbstractCommandline --+

Command line wrapper for clustalw (version one or two).


Last checked against versions: 1.83 and 2.1


Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.


>>> from Bio.Align.Applications import ClustalwCommandline
>>> in_file = "unaligned.fasta"
>>> clustalw_cline = ClustalwCommandline("clustalw2", infile=in_file)
>>> print(clustalw_cline)
clustalw2 -infile=unaligned.fasta

You would typically run the command line with clustalw_cline() or via the Python subprocess module, as described in the Biopython tutorial.

Instance Methods [hide private]
__init__(self, cmd='clustalw', **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='clustalw', **kwargs)

source code 
Initialize the class.
Overrides: object.__init__