Package Bio :: Package Blast :: Module Applications :: Class NcbipsiblastCommandline
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Class NcbipsiblastCommandline

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                     object --+                
                              |                
Application.AbstractCommandline --+            
                                  |            
          _NcbibaseblastCommandline --+        
                                      |        
                  _NcbiblastCommandline --+    
                                          |    
                  _Ncbiblast2SeqCommandline --+
                                              |
                                             NcbipsiblastCommandline

Wrapper for the NCBI BLAST+ program psiblast.

With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old blastpgp tool with a similar tool psiblast. This wrapper therefore replaces BlastpgpCommandline, the wrapper for blastpgp.

>>> from Bio.Blast.Applications import NcbipsiblastCommandline
>>> cline = NcbipsiblastCommandline(help=True)
>>> cline
NcbipsiblastCommandline(cmd='psiblast', help=True)
>>> print(cline)
psiblast -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='psiblast', **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='psiblast', **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)