\begin{Verbatim}[commandchars=\\\{\}]
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{Bio} \PYG{k+kn}{import} \PYG{n}{motifs}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}Arnt.sites\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{handle}\PYG{p}{:}
\PYG{g+gp}{... }    \PYG{n}{motif} \PYG{o}{=} \PYG{n}{motifs}\PYG{o}{.}\PYG{n}{read}\PYG{p}{(}\PYG{n}{handle}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}sites\PYGZdq{}}\PYG{p}{)}
\PYG{g+gp}{...}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{motif}\PYG{o}{.}\PYG{n}{counts}\PYG{p}{)}
\PYG{g+go}{        0      1      2      3      4      5}
\PYG{g+go}{A:   4.00  19.00   0.00   0.00   0.00   0.00}
\PYG{g+go}{C:  16.00   0.00  20.00   0.00   0.00   0.00}
\PYG{g+go}{G:   0.00   1.00   0.00  20.00   0.00  20.00}
\PYG{g+go}{T:   0.00   0.00   0.00   0.00  20.00   0.00}
\PYG{g+go}{\PYGZlt{}BLANKLINE\PYGZgt{}}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{motif}\PYG{o}{.}\PYG{n}{pwm}\PYG{p}{)}
\PYG{g+go}{        0      1      2      3      4      5}
\PYG{g+go}{A:   0.20   0.95   0.00   0.00   0.00   0.00}
\PYG{g+go}{C:   0.80   0.00   1.00   0.00   0.00   0.00}
\PYG{g+go}{G:   0.00   0.05   0.00   1.00   0.00   1.00}
\PYG{g+go}{T:   0.00   0.00   0.00   0.00   1.00   0.00}
\PYG{g+go}{\PYGZlt{}BLANKLINE\PYGZgt{}}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{motif}\PYG{o}{.}\PYG{n}{pssm}\PYG{p}{)}
\PYG{g+go}{        0      1      2      3      4      5}
\PYG{g+go}{A:  \PYGZhy{}0.32   1.93   \PYGZhy{}inf   \PYGZhy{}inf   \PYGZhy{}inf   \PYGZhy{}inf}
\PYG{g+go}{C:   1.68   \PYGZhy{}inf   2.00   \PYGZhy{}inf   \PYGZhy{}inf   \PYGZhy{}inf}
\PYG{g+go}{G:   \PYGZhy{}inf  \PYGZhy{}2.32   \PYGZhy{}inf   2.00   \PYGZhy{}inf   2.00}
\PYG{g+go}{T:   \PYGZhy{}inf   \PYGZhy{}inf   \PYGZhy{}inf   \PYGZhy{}inf   2.00   \PYGZhy{}inf}
\PYG{g+go}{\PYGZlt{}BLANKLINE\PYGZgt{}}
\end{Verbatim}
