1st

.gitignore

+*~
+jeter*
+*.aux
+*.log
+*.out
+*.pdf
+xml01.png
+

Makefile

+.PHONY:all clean show
+BASENAME=tdncbi
+%.pdf:%.ps
+	ps2pdf $<
+%.pnm:%.jpg
+	jpegtopnm $< > $@
+%.ps:%.pnm
+	pnmtops $< > $@
+%.epsi:%.ps
+	ps2epsi $<
+%.ps:%.svg
+	inkscape --without-gui --export-ps=$@ $<
+%.pnm:%.gif
+	giftopnm $< > $@
+
+show: $(BASENAME).pdf 
+	evince $< &
+
+all: $(BASENAME).pdf 
+
+$(BASENAME).pdf : $(BASENAME).tex xml01.png
+	pdflatex --enable-write18 -interaction=errorstopmode -halt-on-error $<
+
+xml01.png : xml01.dot
+	dot -o $@ -T png $<
+
+clean: 
+	rm -f xml01.png
+	rm -f $(foreach SUF,dvi aux dvi.pdf log nav out ps pdf snm toc vrb, $(BASENAME).$(SUF) ) *~ $(TOREMOVE)

tdncbi.tex

+\documentclass{article}
+\usepackage[utf8]{inputenc}
+\usepackage{hyperref}
+\usepackage{graphicx}
+\usepackage{listings}
+\usepackage{xcolor}
+\usepackage{amssymb}
+\usepackage{framed}
+\usepackage{epstopdf}
+
+ 
+% http://tex.stackexchange.com/questions/4979/convert-gif-image-to-png-on-the-fly
+\epstopdfDeclareGraphicsRule{.gif}{png}{.png}{convert  #1 `basename #1 .gif`-gif-converted-to.png}
+\AppendGraphicsExtensions{.gif}
+
+\lstset{frame=single,backgroundcolor=\color{lightgray}}
+
+
+\newcommand{\remoteimage}[3]{
+\IfFileExists{#1}{}{\immediate\write18{wget -O "#1" "#2"}}
+\begin{center}
+\includegraphics[#3]{#1}
+\end{center}
+}
+
+\newcommand{\graphviz}[3]{
+\IfFileExists{#1}{}{\immediate\write18{echo #2 | dot -o"#1.png" -Tpng}}
+\begin{center}
+\includegraphics[#3]{#1.png}
+\end{center}
+}
+
+\newcommand{\inkscape}[2]{
+\IfFileExists{jeter_svg_#1.png}{}{\immediate\write18{inkscape -z --export-png=jeter_svg_#1.png ../img/svg/#1.svg}}
+\begin{center}
+\includegraphics[#2]{jeter_svg_#1.png}
+\end{center}
+}
+
+
+\newcommand{\code}[1]{`\texttt{#1}`}
+\lstset{frame=single,backgroundcolor=\color{lightgray},numbers=left,breaklines=true,basicstyle=\ttfamily}
+
+
+\title{Advanced NCBI\\M2 Bioinfo Nantes.}
+\author{Pierre Lindenbaum\\\href{https://twitter.com/yokofakun}{@yokofakun}\\ \href{mailto:plindenbaum@yahoo.fr}{pierre.lindenbaum@univ-nantes.fr}\\ \url{http://plindenbaum.blogspot.com}\\\href{https://github.com/lindenb/courses}{https://github.com/lindenb/courses}} 
+
+\date{\today}
+
+\begin{document}
+\maketitle
+\begin{abstract}
+NCBI avancé
+\end{abstract}
+
+\section{Rappels}
+\subsection{XML}
+
+\begin{lstlisting}[language=xml]
+<TSeqSet>
+<TSeq>
+  <TSeq_seqtype value="nucleotide"/>
+  <TSeq_gi>25</TSeq_gi>
+  <TSeq_accver>X53813.1</TSeq_accver>
+  <TSeq_taxid>9771</TSeq_taxid>
+  <TSeq_orgname>Balaenoptera musculus</TSeq_orgname>
+  <TSeq_defline>Blue Whale heavy satellite DNA</TSeq_defline>
+  <TSeq_length>422</TSeq_length>
+  <TSeq_sequence>TAGTTATT(...)CAACCCCA</TSeq_sequence>
+</TSeq>
+</TSeqSet>
+\end{lstlisting}
+
+\includegraphics[scale=0.25]{xml01.png}
+
+\subsection{web et ligne de commande}
+\begin{lstlisting}[language=bash]
+wget -O - "https://en.wikipedia.org/wiki/Main_Page"
+\end{lstlisting}
+
+\begin{lstlisting}[language=bash]
+curl  "https://en.wikipedia.org/wiki/Main_Page"
+\end{lstlisting}
+
+\subsection{xmllint}
+
+Exemple 1:
+\begin{lstlisting}[language=bash]
+curl "https://en.wikipedia.org/wiki/Main_Page" | xmllint   --format -
+\end{lstlisting}
+
+Exemple 2:
+\begin{lstlisting}[language=bash]
+curl "https://en.wikipedia.org/wiki/Main_Page" | xmllint  --xpath '//a/@href' -
+\end{lstlisting}
+
+
+\end{document}
+

xml01.dot

+
+digraph G
+	{
+	idp0 [label="<ROOT>"];
+	idm22816 [label="TSeqSet",shape=oval]
+idm23008 [label="TSeq",shape=oval]
+idp117472 [label="TSeq_seqtype",shape=oval]
+idp116664 [label="@value=nucleotide",shape=box]
+idp116664 -> idp117472;
+idp117472 -> idm23008;
+idp198184 [label="TSeq_gi",shape=oval]
+idp198248 [label="25",shape=plaintext]
+idp198248 -> idp198184;
+idp198184 -> idm23008;
+idp200344 [label="TSeq_accver",shape=oval]
+idp200408 [label="X53813.1",shape=plaintext]
+idp200408 -> idp200344;
+idp200344 -> idm23008;
+idp200536 [label="TSeq_taxid",shape=oval]
+idp200600 [label="9771",shape=plaintext]
+idp200600 -> idp200536;
+idp200536 -> idm23008;
+idp200728 [label="TSeq_orgname",shape=oval]
+idp200792 [label="Balaenoptera musculu...",shape=plaintext]
+idp200792 -> idp200728;
+idp200728 -> idm23008;
+idp200920 [label="TSeq_defline",shape=oval]
+idp200984 [label="Blue Whale heavy sat...",shape=plaintext]
+idp200984 -> idp200920;
+idp200920 -> idm23008;
+idp201112 [label="TSeq_length",shape=oval]
+idp201176 [label="422",shape=plaintext]
+idp201176 -> idp201112;
+idp201112 -> idm23008;
+idp201304 [label="TSeq_sequence",shape=oval]
+idp201368 [label="TAGTTATTCAACCTATCCCA...",shape=plaintext]
+idp201368 -> idp201304;
+idp201304 -> idm23008;
+idm23008 -> idm22816;
+idm22816 -> idp0;
+
+	}