Package Bio :: Package Blast :: Module Applications :: Class NcbiblastnCommandline
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Class NcbiblastnCommandline

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

Wrapper for the NCBI BLAST+ program blastn (for nucleotides).

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 blastn.

For example, to run a search against the "nt" nucleotide database using the
FASTA nucleotide file "m_code.fasta" as the query, with an expectation value
cut off of 0.001, saving the output to a file in XML format:

>>> from Bio.Blast.Applications import NcbiblastnCommandline
>>> cline = NcbiblastnCommandline(query="m_cold.fasta", db="nt", strand="plus",
...                               evalue=0.001, out="m_cold.xml", outfmt=5)
>>> cline
NcbiblastnCommandline(cmd='blastn', out='m_cold.xml', outfmt=5, query='m_cold.fasta', db='nt', evalue=0.001, strand='plus')
>>> print(cline)
blastn -out m_cold.xml -outfmt 5 -query m_cold.fasta -db nt -evalue 0.001 -strand plus

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='blastn', **kwargs)
Create a new instance of a command line wrapper object.
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_validate(self)
Make sure the required parameters have been set (PRIVATE).
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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='blastn', **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)