Package Bio :: Package Blast :: Module Applications :: Class NcbiblastpCommandline
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Class NcbiblastpCommandline

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                     object --+                    
                              |                    
Application.AbstractCommandline --+                
                                  |                
          _NcbibaseblastCommandline --+            
                                      |            
                  _NcbiblastCommandline --+        
                                          |        
                  _Ncbiblast2SeqCommandline --+    
                                              |    
                  _NcbiblastMain2SeqCommandline --+
                                                  |
                                                 NcbiblastpCommandline

Create a commandline for the NCBI BLAST+ program blastp (for proteins).

With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old blastall tool with separate tools for each of the searches. This wrapper therefore replaces BlastallCommandline with option -p blastp.

>>> from Bio.Blast.Applications import NcbiblastpCommandline
>>> cline = NcbiblastpCommandline(query="rosemary.pro", db="nr",
...                               evalue=0.001, remote=True, ungapped=True)
>>> cline
NcbiblastpCommandline(cmd='blastp', query='rosemary.pro', db='nr', evalue=0.001, remote=True, ungapped=True)
>>> print(cline)
blastp -query rosemary.pro -db nr -evalue 0.001 -remote -ungapped

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='blastp', **kwargs)
Create a new instance of a command line wrapper object.
source code

Inherited from _NcbiblastMain2SeqCommandline (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='blastp', **kwargs)
(Constructor)

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