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

Class NcbiblastpCommandline

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

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

source code

Inherited from Application.AbstractCommandline: __repr__, __setattr__, __str__, set_parameter

Inherited from Application.AbstractCommandline (private): _check_value, _clear_parameter, _get_parameter

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __sizeof__, __subclasshook__