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

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

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 cline() or via the Python subprocess module, as described in the Biopython tutorial.

Instance Methods [hide private]
__init__(self, cmd='blastx', **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='blastx', **kwargs)

source code 
Initialize the class.
Overrides: object.__init__