Package Bio :: Package Blast :: Module Applications :: Class BlastpgpCommandline
[hide private]
[frames] | no frames]

Class BlastpgpCommandline

source code

                     object --+            
                              |            
Application.AbstractCommandline --+        
                                  |        
                  _BlastCommandLine --+    
                                      |    
              _BlastAllOrPgpCommandLine --+
                                          |
                                         BlastpgpCommandline

Create a commandline for the blastpgp program from NCBI (OBSOLETE).

With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI
are replacing blastpgp with a renamed tool psiblast. This module provides
NcbipsiblastCommandline as a wrapper for the new tool psiblast.

Like blastpgp (and blastall), this wrapper is now obsolete, and will be
deprecated and removed in a future release of Biopython.

>>> from Bio.Blast.Applications import BlastpgpCommandline
>>> cline = BlastpgpCommandline(help=True)
>>> cline
BlastpgpCommandline(cmd='blastpgp', help=True)
>>> print(cline)
blastpgp --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='blastpgp', **kwargs)
Create a new instance of a command line wrapper object.
source code

Inherited from _BlastCommandLine (private): _validate

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='blastpgp', **kwargs)
(Constructor)

source code 
Create a new instance of a command line wrapper object.

Overrides: object.__init__
(inherited documentation)