Class ClustalwCommandline
source code
object --+
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Application.AbstractCommandline --+
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ClustalwCommandline
Command line wrapper for clustalw (version one or two).
http://www.clustal.org/
Example:
>>> 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.
Citation:
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 2.0.10
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__init__(self,
cmd=' clustalw ' ,
**kwargs)
Create a new instance of a command line wrapper object. |
source code
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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__
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Inherited from object :
__class__
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__init__(self,
cmd=' clustalw ' ,
**kwargs)
(Constructor)
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Create a new instance of a command line wrapper object.
- Overrides:
object.__init__
- (inherited documentation)
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