Commit 4db94baa authored by lindenb's avatar lindenb
Browse files

1st

parents
*~
jeter*
*.aux
*.log
*.out
*.pdf
xml01.png
.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)
\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}
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;
}
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