Package Bio :: Package Align :: Package Applications :: Module _ClustalOmega :: Class ClustalOmegaCommandline
[hide private]
[frames] | no frames]

Class ClustalOmegaCommandline

source code

                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 ClustalOmegaCommandline

Command line wrapper for clustal omega

http://www.clustal.org/omega

Example:

>>> from Bio.Align.Applications import ClustalOmegaCommandline
>>> in_file = "unaligned.fasta"
>>> out_file = "aligned.fasta"
>>> clustalomega_cline = ClustalOmegaCommandline(infile=in_file, outfile=out_file, verbose=True, auto=True)
>>> print(clustalomega_cline)
clustalo -i unaligned.fasta -o aligned.fasta --auto -v

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

Citation:

Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7:539 doi:10.1038/msb.2011.75

Last checked against versions: 1.2.0

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

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