Package Bio :: Package Align :: Package Applications :: Module _Dialign :: Class DialignCommandline
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Class DialignCommandline

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                     object --+    
Application.AbstractCommandline --+

Command line wrapper for the multiple alignment program DIALIGN2-2.


Last checked against version: 2.2


B. Morgenstern (2004). DIALIGN: Multiple DNA and Protein Sequence Alignment at BiBiServ. Nucleic Acids Research 32, W33-W36.


To align a FASTA file (unaligned.fasta) with the output files names aligned.* including a FASTA output file (aligned.fa), use:

>>> from Bio.Align.Applications import DialignCommandline
>>> dialign_cline = DialignCommandline(input="unaligned.fasta",
...                                    fn="aligned", fa=True)
>>> print(dialign_cline)
dialign2-2 -fa -fn aligned unaligned.fasta

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

Instance Methods [hide private]
__init__(self, cmd='dialign2-2', **kwargs)
Initialize the class.
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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__

Class Variables [hide private]

Inherited from Application.AbstractCommandline: parameters

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, cmd='dialign2-2', **kwargs)

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Initialize the class.
Overrides: object.__init__