Package Bio :: Package Align :: Package Applications :: Module _TCoffee :: Class TCoffeeCommandline
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Class TCoffeeCommandline

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                     object --+    
                              |    
Application.AbstractCommandline --+
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                                 TCoffeeCommandline

Commandline object for the TCoffee alignment program.

http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html

The T-Coffee command line tool has a lot of switches and options. This wrapper implements a VERY limited number of options - if you would like to help improve it please get in touch.

Example:

To align a FASTA file (unaligned.fasta) with the output in ClustalW format (file aligned.aln), and otherwise default settings, use:

>>> from Bio.Align.Applications import TCoffeeCommandline
>>> tcoffee_cline = TCoffeeCommandline(infile="unaligned.fasta",
...                                    output="clustalw",
...                                    outfile="aligned.aln")
>>> print(tcoffee_cline)
t_coffee -output clustalw -infile unaligned.fasta -outfile aligned.aln

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

Citation:

T-Coffee: A novel method for multiple sequence alignments. Notredame, Higgins, Heringa, JMB,302(205-217) 2000

Last checked against: Version_6.92

Instance Methods [hide private]
 
__init__(self, cmd='t_coffee', **kwargs)
Create a new instance of a command line wrapper object.
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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]
  SEQ_TYPES = ['dna', 'protein', 'dna_protein']
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

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

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Create a new instance of a command line wrapper object.

Overrides: object.__init__
(inherited documentation)