34_clover_pallescens.Rnw

%% LyX 2.0.6 created this file.  For more info, see http://www.lyx.org/.
%% Do not edit unless you really know what you are doing.
\documentclass{article}
\usepackage[sc]{mathpazo}
\usepackage[T1]{fontenc}
\usepackage{geometry}
\geometry{verbose,tmargin=2.5cm,bmargin=2.5cm,lmargin=2.5cm,rmargin=2.5cm}
\usepackage{url}
\usepackage[unicode=true,pdfusetitle,
 bookmarks=true,bookmarksnumbered=true,bookmarksopen=true,bookmarksopenlevel=2,
 breaklinks=false,pdfborder={0 0 1},backref=false,colorlinks=false]
 {hyperref}
\hypersetup{
 pdfstartview={XYZ null null 1}}
\usepackage{listings}
\lstloadlanguages{Python}
\usepackage{pgfplotstable}
\usepackage{csvsimple}


\begin{document}
\definecolor{keywords}{RGB}{255,0,90}
\definecolor{comments}{RGB}{0,0,113}
\definecolor{red}{RGB}{160,0,0}
\definecolor{green}{RGB}{0,150,0}
 
 
\lstset{framextopmargin=50pt}
\lstset{language=Python, 
        basicstyle=\ttfamily\small, 
        keywordstyle=\color{keywords},
        commentstyle=\color{comments},
        stringstyle=\color{red},
        showstringspaces=false,
        identifierstyle=\color{green},
        breaklines=true}
        
\renewcommand\thesection{\arabic{section}}

%%% for TOC with numbering

\title{Trifolium Pallescens genome annotation}


\author{Vikas Gupta and Stig U. Andersen}

\maketitle
\setcounter{secnumdepth}{5}
\setcounter{tocdepth}{5}
\tableofcontents
\newpage


% add dot after number
\makeatletter
\g@addto@macro\thesection.
\makeatother

<<setup, include=FALSE, cache=FALSE>>=
library(knitr)
# set global chunk options
opts_chunk$set(fig.path='figure/minimal-', fig.align='center', fig.show='hold')
options(replace.assign=TRUE,width=90)
@

\section{Data}

<<FileSummary, include=TRUE,cache=TRUE>>=
# p <- path.expand("/Volumes/GenomeDK/LotusGenome/01_vgupta/11_clover/20140709_clover_pallescens/RogerMoraga")
# setwd(p)
# p
# ## File size
# a <- system("ls -lh | awk '{print $9,$5}'",intern=TRUE)
# 
# for (i in a){
#     print (i)
# }
# 
# @

\end{document}