Commit 4a2cee14 authored by Laros's avatar Laros
Browse files

Added packages slides.

parent b9b88744
../../submodules/presentation/Makefile
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../../submodules/presentation/beamerthemelumc.sty
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\documentclass[slidestop]{beamer}
\title{Python Packages of Popular Programs}
\providecommand{\myConference}{Work discussion}
\providecommand{\myDate}{Wednesday, 8 May 2013}
\author{Jeroen F. J. Laros}
\providecommand{\myGroup}{Leiden Genome Technology Center}
\providecommand{\myDepartment}{Department of Human Genetics}
\providecommand{\myCenter}{Center for Human and Clinical Genetics}
\providecommand{\lastCenterLogo}{
\raisebox{-0.1cm}{
\includegraphics[height = 1cm]{lgtc_logo}
%\includegraphics[height = 0.7cm]{ngi_logo}
}
}
\providecommand{\lastRightLogo}{
%\includegraphics[height = 0.7cm]{nbic_logo}
%\includegraphics[height = 0.8cm]{nwo_logo_en}
%\hspace{1.5cm}\includegraphics[height = 0.7cm]{gen2phen_logo}
}
\usetheme{lumc}
\begin{document}
% This disables the \pause command, handy in the editing phase.
%\renewcommand{\pause}{}
% Make the title page.
\bodytemplate
% First page of the presentation.
\section{Introduction}
\begin{frame}[fragile]
\frametitle{Distributing programs}
Via PyPI - the Python Package Index.
\bigskip
\begin{itemize}
\item Anyone can install your software easily.
\item Dependencies are automatically installed.
\item No more sharing of scripts.
\begin{itemize}
\item \ldots that need the help of the developer to run.
\end{itemize}
\end{itemize}
\bigskip
\bigskip
\pause
\begin{lstlisting}[language=bash]
pip install tssv
\end{lstlisting}
\end{frame}
%\begin{frame}
% \frametitle{The problem with scripts.}
%\end{frame}
%
%\begin{frame}
% \frametitle{Solution for source.}
%\end{frame}
%
%\begin{frame}
% \frametitle{The problem with distributing source.}
%\end{frame}
%
%\section{Packages}
%\begin{frame}
% \frametitle{Professional distribution.}
%
% Make things so easy for the end-user that they will not share programs.
%\end{frame}
\section{LUMC packages}
\begin{fframe}
\frametitle{Released packages}
We currently have released the following packages:
\begin{itemize}
\item wiggelen
\item fastools
\item piletools
\item barcode
\item tssv
\item kMer
\end{itemize}
\vfill
\permfoot{https://pypi.python.org/}
\end{fframe}
\begin{fframe}
\frametitle{wiggelen}
Working with wiggle tracks in Python.
\begin{table}[]
\begin{center}
\begin{tabular}{lp{7cm}}
command & explanation\\
\hline
\bt{index} & build index for wiggle track\\
\bt{sort} & sort wiggle track regions alphabetically\\
\bt{scale} & scale values in a wiggle track\\
\bt{merge} & merge wiggle tracks in various ways\\
\bt{distance} & calculate distances between tracks\\
\bt{coverage} & convert a track to coverage intervals\\
\bt{derivative} & create derivative of a wiggle track
\end{tabular}
\end{center}
\caption{Functionality of \bt{wiggelen}.}
\label{}
\end{table}
\vfill
Obsoletes: \bs{wiggledist}, \bs{wigglemerge}, \bs{wiggle2region}.
\end{fframe}
\begin{fframe}
\frametitle{piletools}
Toolkit for the analysis of pileup files (depends on \bt{wiggelen}).
\begin{table}[]
\begin{center}
\begin{tabular}{lp{7cm}}
command & explanation\\
\hline
\bt{mpileup2wig} & convert an mpileup file to to a wiggle file\\
\bt{mpileup2tagwig} & record 5' or 3' ends of reads, strand specific
\end{tabular}
\end{center}
\caption{Functionality of \bt{piletools}.}
\label{}
\end{table}
\vfill
Obsoletes: \bs{mpileup2wig}, \bs{sageWiggle}.
\end{fframe}
\begin{fframe}
\frametitle{fastools}
Toolkit for the analysis and manipulation of FASTA/Q files.
\begin{table}[]
\begin{center}
\begin{tabular}{ll}
command & explanation\\
\hline
sanitise & convert to standard FASTA/FASTQ\\
add & add a '5 sequence\\
select & select a part of every sequence\\
get & retrieve a sequence from the NCBI\\
lenfilt & split a FASTA/FASTQ file based on length
\end{tabular}
\end{center}
\caption{Highlights of \bt{fastools}.}
\label{}
\end{table}
\vfill
Obsoletes: \bs{fa2fa}, \bs{fa2fq}, \bs{fq2fa},
\bs{GAPSS\_add\_5prime\_sequence\_v2\_Sanger}, \bs{alignRefSeqs},
\bs{restrict}, \bs{collapse}, \bs{sanger2illumina}, \bs{select},
\bs{fa2gb}, \bs{gb2fa}, \bs{fastaMangle}, \bs{generateDNA},
\bs{getReference}, \bs{lengthFilter}, \bs{ngslib}
\end{fframe}
\begin{fframe}
\frametitle{fastools}
Also includes a demultiplexer.
\begin{itemize}
\item Allows for mismatches (default $1$).
\item Guess barcodes (supply amount and sample size).
\item Read barcodes from a file.
\begin{itemize}
\item Give barcodes a name.
\end{itemize}
\item Cut a barcode from a read.
\begin{itemize}
\item Optionally select which part needs to be saved.
\end{itemize}
\end{itemize}
\vfill
Obsoletes: \bs{demultiplex}.
\end{fframe}
\section{Questions?}
\lastpagetemplate
\begin{frame}
\begin{center}
Acknowledgements:
\bigskip
\bigskip
Martijn Vermaat
Yahya Anvar
Johan den Dunnen
\end{center}
\end{frame}
\end{document}
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