Class NcbiblastnCommandline

source code

                     object --+            
                              |            
Application.AbstractCommandline --+        
                                  |        
              _NcbiblastCommandline --+    
                                      |    
              _Ncbiblast2SeqCommandline --+
                                          |
                                         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', query='m_cold.fasta', db='nt', out='m_cold.xml', evalue=0.001, outfmt=5, strand='plus')
>>> print cline
blastn -query m_cold.fasta -db nt -out m_cold.xml -evalue 0.001 -outfmt 5 -strand plus

You would typically run the command line with the Python subprocess module, as described in the Biopython tutorial.