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

Class ClustalOmegaCommandline

source code

                     object --+    
Application.AbstractCommandline --+

Command line wrapper for clustal omega


>>> 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.


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)

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