Package Bio :: Package Align :: Package Applications :: Module _Prank :: Class PrankCommandline
[hide private]
[frames] | no frames]

Class PrankCommandline

source code

                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 PrankCommandline

Command line wrapper for the multiple alignment program PRANK.

http://www.ebi.ac.uk/goldman-srv/prank/prank/

Example:

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.

Citations:

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.

Last checked against version: 081202

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

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, cmd='prank', **kwargs)
(Constructor)

source code 
Create a new instance of a command line wrapper object.
Overrides: object.__init__
(inherited documentation)