Package Bio :: Package Align :: Package Applications :: Module _Clustalw :: Class ClustalwCommandline
[hide private]
[frames] | no frames]

Class ClustalwCommandline

source code

                     object --+    
Application.AbstractCommandline --+

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


>>> 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.


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.

Last checked against versions: 1.83 and 2.1

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

source code 
Create a new instance of a command line wrapper object.

Overrides: object.__init__
(inherited documentation)