Pierre Lindenbaum lindenb

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I hate people.

Institut-du-Thorax, Nantes, France.

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lindenb / discordant.c

Created April 12, 2019 07:26

C program finding discordant reads. htslib sam bam read sv structural variant

	/**
	Pierre Lindenbaum, 2019

	gcc -o a.out -O3 -Wall -Isamtools/include discordant.c -Lsamtools/lib -lhts

	*/
	#include <stdio.h>
	#include <stdlib.h>
	#include <errno.h>
	#include <string.h>

lindenb / tmp.c

Created March 25, 2019 16:34

bam x11

	#include <X11/Xlib.h>
	#include <cstdio>
	#include <cstdlib>
	#include <cstring>
	#include <string>
	#include <vector>
	#include <iostream>
	#include <fstream>
	#include <limits.h>
	#include <unistd.h>

lindenb / README.md

Created March 21, 2019 11:37

"custom module" modulepath path

create directory

mkdir -p .modulefiles/reference/human

create the module file .modulefiles/reference/human/GRCh37.75.lua

lindenb / README.md

Created March 11, 2019 16:48

https://www.biostars.org/p/368754/ jvarkit java bed bam

usage:

$ ls input.bed
$ java -jar dist/samjdk.jar --body -f biostar368754.code input.bam

lindenb / README.md

Created March 5, 2019 20:56

https://www.biostars.org/p/367522 Plotting overlapping genomic segments in R :: svg xml

echo -e '@HD\tVN:1.4\tSO:unsorted\n@SQ\tSN:2\tLN:243199373' > tmp.dict &&  \
java -jar dist/biostar336589.jar -a 60 -R tmp.dict <(grep -v Chr input.bed)  > out.svg

lindenb / README.md

Last active February 22, 2019 14:49

https://www.biostars.org/p/365479/ Question: Bioinformatics word cloud to use in classes bioinformatics xml pubmed ncbi cloud word xslt jvarkit

Example

Mesh words in 'Oxford Bioinformatics' 2018.

 java -jar dist/pubmeddump.jar 'Bioinformatics[journal] AND 2018[PDAT]'| \
 java -jar dist/xsltstream.jar --tag PubmedArticle -t biostars365479.xsl > out.txt

lindenb / biostars365290.xsl

Created February 21, 2019 17:52

Question: Retrieving assembly statistics for several accessions https://www.biostars.org/p/365290/ ncbi xsl xslt xml genome assembly

	<?xml version='1.0' encoding="UTF-8" ?>
	<xsl:stylesheet
	xmlns:xsl='http://www.w3.org/1999/XSL/Transform'
	xmlns:h='http://www.w3.org/1999/xhtml'
	version='1.0'>
	<xsl:output method="text"/>


	<xsl:template match="/">
	<xsl:apply-templates select="//h:table[@summary='Global statistics']/h:tbody/h:tr"/>

lindenb / biostar69995.xsl

Created February 15, 2019 11:14

https://www.biostars.org/p/69995/ sra ncbi xslt xsl sql

	<?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"/>
	<xsl:template match="/">
	create table if not exists EXPERIMENT
	(
	id INTEGER PRIMARY KEY AUTOINCREMENT,
	alias TEXT,
	center_name TEXT,

lindenb / pubmed.user.js

Created February 7, 2019 12:07

Greasemonkey script adding link to pubmed2bibtex pubmed ncbi tex bibtex greasemonkey user script

	// ==UserScript==
	// @description Display posts of a reddit user
	// @grant none
	// @include https://www.ncbi.nlm.nih.gov/pubmed*
	// @name pubmed
	// @namespace https://github.com/lindenb/greasemonkey
	// ==/UserScript==

	var array=[];
	var iter = document.evaluate("//p/a[starts-with(@href,'/pubmed?linkname=pubmed_pubmed&from_uid=') and text()='Similar articles']",document,null,XPathResult.UNORDERED_NODE_ITERATOR_TYPE, null);

lindenb / biostar362495.xsl

Created February 7, 2019 10:07

https://www.biostars.org/p/362495/ biostars filter blastp blast xslt xslt xml

	<?xml version='1.0' encoding="UTF-8" ?>
	<xsl:stylesheet
	xmlns:xsl='http://www.w3.org/1999/XSL/Transform'
	version='1.0'
	>
	<xsl:output method="xml" encoding="UTF-8"/>


	<xsl:template match="*">
	<xsl:copy>

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