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

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                     object --+    
Application.AbstractCommandline --+

Commandline object for the TCoffee alignment program.

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.


Last checked against: Version_6.92


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


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.

Instance Methods [hide private]
__init__(self, cmd='t_coffee', **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]
  SEQ_TYPES = ['dna', 'protein', 'dna_protein']

Inherited from Application.AbstractCommandline: parameters

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

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

source code 
Initialize the class.
Overrides: object.__init__