intro_python_trii_4.tex

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\newcommand{\thankyou}
{\begin{center} Would love to hear your experience! \\  gabow@cbio.mskcc.org \\ vipin@cbio.mskcc.org \end{center}}
%
\title[pyClass1]{Introduction to Programming with Python - Day 4}
\author{vipin@cbio.mskcc.org}
%
\institute[cBio@MSKCC]
{
    R{\"a}tsch Laboratory, Computational Biology Center\\
    Memorial Sloan Kettering Cancer Center\\
}
\date{13 November 2014}
%
\begin{document}
\maketitle
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\begin{frame}[plain]
    \frametitle{Python for Scientific Computing}
    \begin{itemize}
        \item[] SciPy is a Python-based ecosystem of open-source software for science. 
        \newline 
        \pause 
        \item[] NumPy - Powerful N-dimensional array object 
        \newline
        \pause
        \item[] Matplotlib - 2D plotting library
        \newline
        \pause
        \item[] IPython - Interactive python console
        \newline
        \pause
        \item[] pandas - Data structures
    \end{itemize}
\end{frame}
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%
\begin{frame}[plain]
    \frametitle{NumPy - multidimensional data arrays}
    \begin{itemize}
        \item[] The \textbf{numpy} package (module) is used in almost all numerical computation using Python.
        \newline
        \pause
        \item[] Provide high-performance vector, matrix and higher-dimensional data structures for Python.
        \newline
        \pause 
        \item[] In the \textbf{numpy} package the terminology used for vectors, matrices and higher-dimensional data sets is \textit{array}.
        \newline
        \pause 
         \lstinputlisting[language=Python]{scripts/import_np_1.py}
         \pause
         \item[] The recommended convention to import numpy is:
        \newline
         \pause
         \lstinputlisting[language=Python]{scripts/import_np_2.py}
    \end{itemize}
\end{frame}
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\begin{frame}[plain]
    \frametitle{NumPy - manual construction of arrays}
    \begin{itemize}
        \item[] 1-Dimension: 
         \lstinputlisting[language=Python]{scripts/np_1d.py}
        \pause 
        \item[] 2-Dimension: 
         \lstinputlisting[language=Python]{scripts/np_2d.py}
    \end{itemize}
\end{frame}
%
\begin{frame}[plain]
    \frametitle{NumPy - basic data types}
    \begin{itemize}
        \item[] Different data types allows to store data efficiently.
        \newline
        \pause
         \lstinputlisting[language=Python]{scripts/np_dtype_1.py}
         \pause
         \item[] ValueError - assign a value of the wrong type to an element
         \lstinputlisting[language=Python]{scripts/np_dtype_2.py}
         \pause
         \item[] Other data types: 
        \begin{itemize}
            \item[] Complex 
            \item[] Bool 
            \item[] String
        \end{itemize}
         \pause
        \lstinputlisting[language=Python]{scripts/np_dtype_3.py}
    \end{itemize}
\end{frame}
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\begin{frame}[plain]
    \frametitle{NumPy - function for creating arrays}
    \begin{itemize}
        \item[] arange
        \lstinputlisting[language=Python]{scripts/np_range.py}
        \pause
        \item[] linspace
        \lstinputlisting[language=Python]{scripts/np_linspace.py}
        \pause
        \item[] random
        \lstinputlisting[language=Python]{scripts/np_rand.py}
        \pause
        \lstinputlisting[language=Python]{scripts/np_randn.py}
    \end{itemize}
\end{frame}
%
\begin{frame}[plain]
    \frametitle{NumPy - common arrays}
    \begin{itemize}
        \item[] zeros  
        \lstinputlisting[language=Python]{scripts/np_zeros.py}
        \pause
        \item[] ones 
        \lstinputlisting[language=Python]{scripts/np_ones.py}
        \pause
        \item[] diag  
        \lstinputlisting[language=Python]{scripts/np_diag.py}
        \pause
        \item[] eye   
        \lstinputlisting[language=Python]{scripts/np_eye.py}
        \pause
        \item[] More details: \url{http://wiki.scipy.org/Tentative_NumPy_Tutorial}
    \end{itemize}
\end{frame}
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\begin{frame}[plain]
    \frametitle{NumPy - indexing}
    \begin{itemize}
        \item[] Index elements in an array using the square bracket and indices. 
        \lstinputlisting[language=Python]{scripts/np_idx_1.py}
        \pause
        \lstinputlisting[language=Python]{scripts/np_idx_2.py}
        \pause
        \item[] If we omit an index of a multidimensional array it returns the whole row
        \lstinputlisting[language=Python]{scripts/np_idx_3.py}
        \pause
        \item[] Assigning new values to elements in an array using indexing
        \lstinputlisting[language=Python]{scripts/np_idx_4.py}
    \end{itemize}
\end{frame}
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\begin{frame}[plain]
    \frametitle{NumPy - slicing}
    \begin{itemize}
        \item[] Index slicing syntax \textbf{xm[lower:upper:step]} to extract part of an array. 
        \lstinputlisting[language=Python]{scripts/np_sl_1.py}
        \pause
        \item[] We can omit any of the three parameters in \textbf{xm[lower:upper:step]}
        \lstinputlisting[language=Python]{scripts/np_sl_2.py}
        \pause 
        \item[] Index slicing works exactly the same way for multidimensional arrays.
        \lstinputlisting[language=Python]{scripts/np_sl_3.py}
    \end{itemize}
\end{frame}
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\begin{frame}[plain]
    \frametitle{Matplotlib - basic visualization}
    \begin{itemize}
        \item[] \textit{Matplotlib} is a 2D plotting package.  
        \pause
        \lstinputlisting[language=Python]{scripts/plt_1d.py}
        \pause
        \lstinputlisting[language=Python]{scripts/plt_2d.py}
        \pause
        \item[] Reference: \url{http://matplotlib.org/}\\
        \url{http://web.stanford.edu/~mwaskom/software/seaborn/}
    \end{itemize}
\end{frame}
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\begin{frame}[plain]
    \frametitle{BioPython - python modules for bioinformatics}
    \begin{itemize}
        \item[] A set of free Python modules for working with sequence analysis.
        \newline
        \pause 
        \begin{itemize}
            \item[] AlignIO 
            \item[] SearchIO
            \item[] BioSQL
            \item[] Seq
            \item[] SeqIO
            \item[] SeqRecord
            \newline
            \pause
        \end{itemize}
        \item[] Details: \url{http://biopython.org}
    \end{itemize}
\end{frame}
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\begin{frame}[plain]
    \frametitle{Seq - basic sequence tools}
    \begin{itemize}
        \item[]  BioPython represents sequences with the \textbf{Seq} object. 
        \newline
        \pause
        \lstinputlisting[language=Python]{scripts/seq.py}
    \end{itemize}
\end{frame}
%
\begin{frame}[plain]
    \frametitle{SeqIO - basic fileIO}
    \begin{itemize}
        \item[] \textbf{parse} function can handle GenBank, FastQ, Fasta formats.  
        \newline
        \pause
        \lstinputlisting[language=Python]{scripts/seqIO.py}
        \pause
        \lstinputlisting[language=Python]{scripts/seqIOfq.py}
    \end{itemize}
\end{frame}
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\begin{frame}[plain]
    \frametitle{SeqRecord - handling sequence records}
    \begin{itemize}
        \item[] Hold a sequence (as a Seq object) with identifiers (ID and name).
        \pause
        \lstinputlisting[language=Python]{scripts/seqrecord.py}
    \end{itemize}
\end{frame}
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\begin{frame}[plain]
    \frametitle{GFF Parsing - parsing genome annotation file}
    \begin{itemize}
        \item[] Not yet integrated into the core biopython  
        \item[] \url{http://github.com/chapmanb/bcbb/tree/master/gff}  
        \newline
        \pause
        \item[] Collection of different annotation conveter programs 
        \item[] \url{https://github.com/vipints/GFFtools-GX} 
    \end{itemize}
\end{frame}
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\begin{frame}[plain]
    \frametitle{\textbf{pip} or \textbf{easy\_install} - managing local python packages}
    \begin{itemize}
        \item[] Machine learning toolbox in python
        \begin{itemize}
            \item []SHOGUN - \url{shogun-toolbox.org}
            \item []scikit-learn - \url{scikit-learn.org} 
        \pause
        \end{itemize}
        \lstinputlisting[language=Bash]{scripts/pip_install.sh}
    \end{itemize}
\end{frame}
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\begin{frame}[plain]
    \frametitle{\textbf{cPickle} - data persistence}
    \begin{itemize}
        \item[] Methods \textbf{dump()}, \textbf{load()} 
        \newline
        \pause
        \lstinputlisting[language=Python]{scripts/cpickle_dump.py}
        \pause
        \lstinputlisting[language=Python]{scripts/cpickle_load.py}
    \end{itemize}
\end{frame}
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\begin{frame}[plain]
    \frametitle{\textbf{Django} - python web framework}
    \begin{itemize}
        \item[] Creating a project: django-admin.py startproject mysite 
        \newline
        \pause 
        \item[] Add names to \textit{mysite settings.py} \textit{mysite urls.py} 
        \pause 
        \item[] python manage.py startapp app\_name
        \pause 
        \item[] Edit view.py 
        \lstinputlisting[language=Python]{scripts/views.py}
        \pause 
        \item[] python manage.py runserver
        \item[] Details: \url{https://www.djangoproject.com/}
    \end{itemize}
\end{frame}
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\begin{frame}[plain]
    \thankyou
\end{frame}
\end{document}