25 March 2013

Embedding Pubmed, Graphiviz and a remote image in #LaTeX. My notebook. .

I'm learning LaTeX. Today I learned how to create a new command in LaTeX.

\newcommand{name}[num]{definition}
"Basically the command requires two arguments: the name of the command you want to create, and the definition of the command" . I played with LaTeX and wrote the following three commands:

Embedding a remote picture

The following LaTeX document defines a new command "\remoteimage". It takes 3 parameters: a filename, a URL and some parameters for \includegraphics. If the file doesn't exist, the url is downloaded and saved in 'file'. The downloaded image is then included in the final LaTeX document.
\documentclass{article}
\usepackage{hyperref}
\usepackage{graphicx}
\newcommand{\remoteimage}[3]{
\IfFileExists{#1}{}{\immediate\write18{curl -o "#1" "#2"}}
\begin{center}
\includegraphics[#3]{#1}
\end{center}
}
\begin{document}
\title{\LaTeX : test with an external Image}
\author{Pierre Lindenbaum\\\href{https://twitter.com/yokofakun}{@yokofakun}\\ \url{http://plindenbaum.blogspot.com} }
\maketitle
\begin{center}
\remoteimage{tmp1.jpg}{http://upload.wikimedia.org/wikipedia/commons/2/2e/Charles_Darwin_seated_crop.jpg}{scale=0.1}
Charles Darwin. Image via wikipedia.
\end{center}
\end{document}
view raw remoteimage.tex hosted with ❤ by GitHub

Note: latex files must be compiled with --enable-write18 to enable system-calls.
pdflatex --enable-write18 input.tex
Result:

External Image /Latex by lindenb


GraphViz Dot

The second LaTex Document works the same way. It defines a command "\graphviz" , sends the content of the 2nd argument to graphviz dot and save the resulting image before importing it into the LaTeX document.
\documentclass{article}
\usepackage{hyperref}
\usepackage{graphicx}
\newcommand{\graphviz}[3]{
\IfFileExists{#1}{}{\immediate\write18{echo #2 | dot -o"#1.png" -Tpng}}
\begin{center}
\includegraphics[#3]{#1.png}
\end{center}
}
\begin{document}
\title{\LaTeX : test with GraphViz}
\author{Pierre Lindenbaum\\\href{https://twitter.com/yokofakun}{@yokofakun}\\ \url{http://plindenbaum.blogspot.com} }
\maketitle
\graphviz{tmpDot}{'digraph G { t9592[label="Gorilla"];t207598[label="Homininae"]; t9606[label="Homo sapiens"]; t9605[label="Homo"];t9604[label="Hominidae"]; t9606 -> t9605; t9605->t207598 ; t9592 -> t207598; t207598->t9604}'}{scale=0.4}
\end{document}
view raw graphviz.tex hosted with ❤ by GitHub

Result:

GraphViz / Latex by lindenb


Pubmed

The last command define "\pmid" . It needs one Pubmed identifer. It downloads the XML record for this pmid, transforms it to LaTeX with xsltproc and the following XSLT stylesheet:
<?xml version='1.0' encoding="ISO-8859-1"?>
<xsl:stylesheet xmlns:xsl='http://www.w3.org/1999/XSL/Transform' version='1.0'
>
<xsl:output method="text" encoding="UTF-8"/>
<xsl:template match="/">
<xsl:apply-templates select="PubmedArticleSet/PubmedArticle/MedlineCitation/Article"/>
</xsl:template>
<xsl:template match="Article">
\section{<xsl:apply-templates select="ArticleTitle"/>}
<xsl:apply-templates select="AuthorList"/>\\
\emph{"<xsl:apply-templates select="Journal/Title"/>"}. {\bf vol. <xsl:apply-templates select="Journal/JournalIssue/Volume"/> }. <xsl:apply-templates select="Journal/JournalIssue/Issue"/>. (<xsl:apply-templates select="Journal/JournalIssue/PubDate/Year"/>). \\
<xsl:apply-templates select="Affiliation"/>\\
\url{http://www.ncbi.nlm.nih.gov/pubmed/<xsl:value-of select="../PMID"/>}\\
<xsl:if test="Abstract/AbstractText">
\begin{shaded}
<xsl:apply-templates select="Abstract/AbstractText"/>
\end{shaded}
</xsl:if>
</xsl:template>
<xsl:template match="AuthorList">
<xsl:text>{\bf </xsl:text>
<xsl:for-each select="Author">
<xsl:choose>
<xsl:when test="position()=1"></xsl:when>
<xsl:when test="position()=last()"> and </xsl:when>
<xsl:otherwise>, </xsl:otherwise>
</xsl:choose>
<xsl:apply-templates select="LastName/text()"/>
<xsl:text> </xsl:text>
<xsl:apply-templates select="Initials/text()"/>
</xsl:for-each>
<xsl:text>}</xsl:text>
</xsl:template>
<!-- copied from https://github.com/Siyavula/siyavula.html2latex/blob/master/templates/xslt/xh2latex.xsl -->
<xsl:template match="text()">
<xsl:call-template name="esc">
<xsl:with-param name="c" select='"#"'/>
<xsl:with-param name="s">
<xsl:call-template name="esc">
<xsl:with-param name="c" select='"$"'/>
<xsl:with-param name="s">
<xsl:call-template name="esc">
<xsl:with-param name="c" select='"%"'/>
<xsl:with-param name="s">
<xsl:call-template name="esc">
<xsl:with-param name="c" select='"&amp;"'/>
<xsl:with-param name="s">
<xsl:call-template name="esc">
<xsl:with-param name="c" select='"~"'/>
<xsl:with-param name="s">
<xsl:call-template name="esc">
<xsl:with-param name="c" select='"_"'/>
<xsl:with-param name="s">
<xsl:call-template name="esc">
<xsl:with-param name="c" select='"^"'/>
<xsl:with-param name="s">
<xsl:call-template name="esc">
<xsl:with-param name="c" select='"{"'/>
<xsl:with-param name="s">
<xsl:call-template name="esc">
<xsl:with-param name="c" select='"}"'/>
<xsl:with-param name="s">
<xsl:call-template name="esc">
<xsl:with-param name="c" select='"\"'/>
<xsl:with-param name="s" select='.'/>
</xsl:call-template>
</xsl:with-param>
</xsl:call-template>
</xsl:with-param>
</xsl:call-template>
</xsl:with-param>
</xsl:call-template>
</xsl:with-param>
</xsl:call-template>
</xsl:with-param>
</xsl:call-template>
</xsl:with-param>
</xsl:call-template>
</xsl:with-param>
</xsl:call-template>
</xsl:with-param>
</xsl:call-template>
</xsl:with-param>
</xsl:call-template>
</xsl:template>
<xsl:template name="esc">
<xsl:param name="s"/>
<xsl:param name="c"/>
<xsl:choose>
<xsl:when test='contains($s, $c)'>
<xsl:value-of select='substring-before($s, $c)'/>
<xsl:text>\</xsl:text>
<xsl:choose>
<xsl:when test='$c = "\"'>
<xsl:text>textbackslash </xsl:text>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select='$c'/>
</xsl:otherwise>
</xsl:choose>
<xsl:call-template name="esc">
<xsl:with-param name='c' select='$c'/>
<xsl:with-param name='s' select='substring-after($s, $c)'/>
</xsl:call-template>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select='$s'/>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
</xsl:stylesheet>
view raw pubmed2tex.xsl hosted with ❤ by GitHub

The LaTeX document includes four pubmed identifiers:
\documentclass{article}
\usepackage{hyperref}
\usepackage{graphicx}
\usepackage{framed}
\usepackage{color}
\usepackage[utf8]{inputenc}
\definecolor{shadecolor}{rgb}{0.9,0.9,0.9}
\newcommand{\pmid}[1]{
\IfFileExists{pmid_#1.tex}{}{\immediate\write18{curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=#1&retmode=xml" | xsltproc --novalid -o pmid_#1.tex pubmed2tex.xsl -}}
\input{pmid_#1.tex}
}
\begin{document}
\title{\LaTeX : test Pubmed/XSLT}
\author{Pierre Lindenbaum\\\href{https://twitter.com/yokofakun}{@yokofakun}\\ \url{http://plindenbaum.blogspot.com} }
\maketitle
\pmid{22046109}
\pmid{21378989}
\pmid{21984761}
\pmid{15047801}
\end{document}
view raw pmid.tex hosted with ❤ by GitHub

Result:

Pumed / Latex by lindenb






That's it,

Pierre




Publié par Pierre Lindenbaum at 9:33 PM 1 commentaires

Libellés : , , , , , , , ,

13 March 2013

Filtering a BAM with javascript.

The following was created to answer that question on biostar: "Exclude reads with XA tag". SamJs is a java program filtering the reads of a BAM file using the javascript engine for java (rhino).

Usage

java -jar samjs.jar [options] (-e script | -f script) (file.bam|stdin)
for each SamRecord in the BAM, the program injects the following variables in the javascript context:
  • 'record' a SamRecord ( http://picard.sourceforge.net/javadoc/net/sf/samtools/SAMRecord.html ).
  • 'header' a SAMFileHeader ( http://picard.sourceforge.net/javadoc/net/sf/samtools/SAMFileHeader.html)

Options

  • -S : SAM output.
  • -e (script).
  • -f (script-file).
  • -L (int) limit to 'L' records.

Example

$ java -jar dist/samjs.jar -L 4  -S \
  -e '(record.inferredInsertSize > 60 || record.alignmentStart  < 50000000) && !record.readUnmappedFlag && record.getAttribute("MD")!=null ' \
 my.bam
@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:247249719
IL31_4368:1:1:997:15684 163 chr1 241356442 60 54M = 241356612 224 CAGCCTCAGATTCAGCATTCTCAAATTCAGCTGCGGCTGAAACAGCAGCAGGAC EEEEDEEE9EAEEDEEEEEEEEEECEEAAEEDEE<CD=D=*BCAC?;CB,<D@, X0:i:1 X1:i:0 MD:Z:53T0 XG:i:0 AM:i:37 NM:i:1 SM:i:37 XM:i:1 XO:i:0 XT:A:U
IL31_4368:1:1:997:1657 163 chr1 143630066 60 54M = 143630364 352 CCCACCTCTCTCAATGTTTTCCATATGGCAGGGACTCAGCACAGGTGGATTAAT A;0A?AA+@A<7A7019/<65,3A;'''07<A=<=>?7=?6&)'9('*%,>/(< X0:i:1 X1:i:0 MD:Z:54 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U
IL31_4368:1:1:999:9391 163 chr1 195364100 29 54M = 195364272 226 AAAAAAAAAAACCCTCATTTTTTTTAAGTACTAAATTTTTTTTCCCATTTGAAA 1>??E?>@BB>0A/43;,=9A98A(',0/<*4>>/@=90A51&(**3;>'*;=; MD:Z:11A5A7C12A2G1A1T1C6 XG:i:0 AM:i:29 NM:i:8 SM:i:29 XM:i:8 XO:i:0 XT:A:M
IL31_4368:1:1:1002:11012 99 chr1 147142473 60 54M = 147142575 156 NGATTAGTACATAGTAAGTACTCAATAGATGTTAGCTATTATTGTAATCACCGC (1*4+236332679?1..87><-6<@<7>>@><7;@@@>962$-6075584093 X0:i:1 X1:i:0 MD:Z:0A40C12 XG:i:0 AM:i:37 NM:i:2 SM:i:37 XM:i:2 XO:i:0 XT:A:U

That's it,
Pierre

Publié par Pierre Lindenbaum at 8:27 PM 0 commentaires

Libellés : , , , ,

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