gistfile1.py

[uzi@quince-srv2 ~/biopython]$ python
Python 2.6.6 (r266:84292, Nov 22 2013, 12:16:22) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio.Blast.Applications import NcbiblastxCommandline
>>> blastx_exec="/home/opt/ncbi-blast-2.2.28+/bin/blastx"
>>> import os
>>> assert os.path.isfile(blastx_exec), "blastx executable missing"
>>> blastx_cline = NcbiblastxCommandline(blastx_exec,query="opuntia.fasta", db="/home/opt/ncbi-blast-2.2.28+/db/nr", evalue=0.001,outfmt=5, out="opuntia.xml")
>>> blastx_cline
NcbiblastxCommandline(cmd='/home/opt/ncbi-blast-2.2.28+/bin/blastx', out='opuntia.xml', outfmt=5, query='opuntia.fasta', db='/home/opt/ncbi-blast-2.2.28+/db/nr', evalue=0.001)
>>> print(blastx_cline)
/home/opt/ncbi-blast-2.2.28+/bin/blastx -out opuntia.xml -outfmt 5 -query opuntia.fasta -db /home/opt/ncbi-blast-2.2.28+/db/nr -evalue 0.001
>>> stdout, stderr = blastx_cline()
>>>