Package Bio :: Package Blast :: Module Applications :: Class NcbirpsblastCommandline
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Class NcbirpsblastCommandline

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                     object --+            
                              |            
Application.AbstractCommandline --+        
                                  |        
          _NcbibaseblastCommandline --+    
                                      |    
                  _NcbiblastCommandline --+
                                          |
                                         NcbirpsblastCommandline

Wrapper for the NCBI BLAST+ program rpsblast.

With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old rpsblast tool with a similar tool of the same name. This wrapper replaces RpsBlastCommandline, the wrapper for the old rpsblast.

>>> from Bio.Blast.Applications import NcbirpsblastCommandline
>>> cline = NcbirpsblastCommandline(help=True)
>>> cline
NcbirpsblastCommandline(cmd='rpsblast', help=True)
>>> print(cline)
rpsblast -help

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

Instance Methods [hide private]
 
__init__(self, cmd='rpsblast', **kwargs)
Create a new instance of a command line wrapper object.
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_validate(self)
Make sure the required parameters have been set (PRIVATE).
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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__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

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

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

_validate(self)

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Make sure the required parameters have been set (PRIVATE).

No return value - it either works or raises a ValueError.

This is a separate method (called from __str__) so that subclasses may override it.

Overrides: Application.AbstractCommandline._validate
(inherited documentation)