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

Class NcbitblastxCommandline

source code

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

Wrapper for the NCBI BLAST+ program tblastx.

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 tblastx.

>>> from Bio.Blast.Applications import NcbitblastxCommandline
>>> cline = NcbitblastxCommandline(help=True)
>>> cline
NcbitblastxCommandline(cmd='tblastx', help=True)
>>> print(cline)
tblastx -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='tblastx', **kwargs)
Initialize the class.
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__

Class Variables [hide private]

Inherited from Application.AbstractCommandline: parameters

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, cmd='tblastx', **kwargs)

source code 
Initialize the class.
Overrides: object.__init__