\begin{Verbatim}[commandchars=\\\{\}]
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{Bio.Blast.Applications} \PYG{k+kn}{import} \PYG{n}{NcbiblastxCommandline}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{help}\PYG{p}{(}\PYG{n}{NcbiblastxCommandline}\PYG{p}{)}
\PYG{g+gp}{...}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{blastx\PYGZus{}cline} \PYG{o}{=} \PYG{n}{NcbiblastxCommandline}\PYG{p}{(}\PYG{n}{query}\PYG{o}{=}\PYG{l+s+s2}{\PYGZdq{}opuntia.fasta\PYGZdq{}}\PYG{p}{,} \PYG{n}{db}\PYG{o}{=}\PYG{l+s+s2}{\PYGZdq{}nr\PYGZdq{}}\PYG{p}{,} \PYG{n}{evalue}\PYG{o}{=}\PYG{l+m+mf}{0.001}\PYG{p}{,}
\PYG{g+gp}{... }                                     \PYG{n}{outfmt}\PYG{o}{=}\PYG{l+m+mi}{5}\PYG{p}{,} \PYG{n}{out}\PYG{o}{=}\PYG{l+s+s2}{\PYGZdq{}opuntia.xml\PYGZdq{}}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{blastx\PYGZus{}cline}
\PYG{g+go}{NcbiblastxCommandline(cmd=\PYGZsq{}blastx\PYGZsq{}, out=\PYGZsq{}opuntia.xml\PYGZsq{}, outfmt=5, query=\PYGZsq{}opuntia.fasta\PYGZsq{},}
\PYG{g+go}{db=\PYGZsq{}nr\PYGZsq{}, evalue=0.001)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{blastx\PYGZus{}cline}\PYG{p}{)}
\PYG{g+go}{blastx \PYGZhy{}out opuntia.xml \PYGZhy{}outfmt 5 \PYGZhy{}query opuntia.fasta \PYGZhy{}db nr \PYGZhy{}evalue 0.001}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{stdout}\PYG{p}{,} \PYG{n}{stderr} \PYG{o}{=} \PYG{n}{blastx\PYGZus{}cline}\PYG{p}{()}
\end{Verbatim}
