Package Bio :: Package Align :: Package Applications :: Module _Prank :: Class PrankCommandline
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Class PrankCommandline

source code

                     object --+    
Application.AbstractCommandline --+

Command line wrapper for the multiple alignment program PRANK.


Last checked against version: 081202


Loytynoja, A. and Goldman, N. 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proceedings of the National Academy of Sciences, 102: 10557--10562.

Loytynoja, A. and Goldman, N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320: 1632.


To align a FASTA file (unaligned.fasta) with the output in aligned FASTA format with the output filename starting with "aligned" (you can't pick the filename explicitly), no tree output and no XML output, use:

>>> from Bio.Align.Applications import PrankCommandline
>>> prank_cline = PrankCommandline(d="unaligned.fasta",
...                                o="aligned", # prefix only!
...                                f=8, # FASTA output
...                                notree=True, noxml=True)
>>> print(prank_cline)
prank -d=unaligned.fasta -o=aligned -f=8 -noxml -notree

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

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

source code 
Initialize the class.
Overrides: object.__init__