Package Bio :: Package Align :: Package Applications :: Module _MSAProbs :: Class MSAProbsCommandline
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Class MSAProbsCommandline

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                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 MSAProbsCommandline

Command line wrapper for MSAProbs.

http://msaprobs.sourceforge.net

Example:

>>> from Bio.Align.Applications import MSAProbsCommandline
>>> in_file = "unaligned.fasta"
>>> out_file = "aligned.cla"
>>> cline = MSAProbsCommandline(infile=in_file, outfile=out_file, clustalw=True)
>>> print(cline)
msaprobs -o aligned.cla -clustalw unaligned.fasta

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

Citation:

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell: "MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities". Bioinformatics, 2010, 26(16): 1958 -1964

Last checked against version: 0.9.7

Instance Methods [hide private]
 
__init__(self, cmd='msaprobs', **kwargs)
Create a new instance of a command line wrapper object.
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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='msaprobs', **kwargs)
(Constructor)

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

Overrides: object.__init__
(inherited documentation)