Package Bio :: Package Blast :: Module Applications :: Class NcbiblastxCommandline
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Class NcbiblastxCommandline

source code

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

Wrapper for the NCBI BLAST+ program blastx (nucleotide query, protein database).

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 blastx.

>>> from Bio.Blast.Applications import NcbiblastxCommandline
>>> cline = NcbiblastxCommandline(query="m_cold.fasta", db="nr", evalue=0.001)
>>> cline
NcbiblastxCommandline(cmd='blastx', query='m_cold.fasta', db='nr', evalue=0.001)
>>> print cline
blastx -query m_cold.fasta -db nr -evalue 0.001

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='blastx', **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: __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='blastx', **kwargs)
(Constructor)

source code 

Create a new instance of a command line wrapper object.

Overrides: object.__init__
(inherited documentation)

_validate(self)

source code 

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)