Class TCoffeeCommandline
source code
object --+
|
Application.AbstractCommandline --+
|
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
|
__init__(self,
cmd=' t_coffee ' ,
**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__
|
|
SEQ_TYPES = [ ' dna ' , ' protein ' , ' dna_protein ' ]
|
Inherited from object :
__class__
|
__init__(self,
cmd=' t_coffee ' ,
**kwargs)
(Constructor)
| source code
|
Create a new instance of a command line wrapper object.
- Overrides:
object.__init__
- (inherited documentation)
|