Package Bio :: Package Align :: Package Applications :: Module _Muscle :: Class MuscleCommandline
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Class MuscleCommandline

source code

                     object --+    
Application.AbstractCommandline --+

Command line wrapper for the multiple alignment program MUSCLE.


Last checked against version: 3.7, briefly against 3.8


Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.

Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1): 113.


>>> from Bio.Align.Applications import MuscleCommandline
>>> muscle_exe = r"C:\Program Files\Aligments\muscle3.8.31_i86win32.exe"
>>> in_file = r"C:\My Documents\unaligned.fasta"
>>> out_file = r"C:\My Documents\aligned.fasta"
>>> muscle_cline = MuscleCommandline(muscle_exe, input=in_file, out=out_file)
>>> print(muscle_cline)
"C:\Program Files\Aligments\muscle3.8.31_i86win32.exe" -in "C:\My Documents\unaligned.fasta" -out "C:\My Documents\aligned.fasta"

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

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

source code 
Initialize the class.
Overrides: object.__init__