KnownGenesToBed

##Motivation

converts UCSC knownGenes file to BED.

##Compilation

Requirements / Dependencies

• java compiler SDK 1.8 http://www.oracle.com/technetwork/java/index.html (NOT the old java 1.7 or 1.6) . Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
• GNU Make >= 3.81
• curl/wget
• git
• xsltproc http://xmlsoft.org/XSLT/xsltproc2.html (tested with "libxml 20706, libxslt 10126 and libexslt 815")

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make kg2bed

by default, the libraries are not included in the jar file, so you shouldn't move them (https://github.com/lindenb/jvarkit/issues/15#issuecomment-140099011 ). You can create a bigger but standalone executable jar by adding standalone=yes on the command line:

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make kg2bed standalone=yes

The required libraries will be downloaded and installed in the dist directory.

edit 'local.mk' (optional)

The a file local.mk can be created edited to override/add some definitions.

For example it can be used to set the HTTP proxy:

http.proxy.host=your.host.com
http.proxy.port=124567

##Synopsis

$ java -jar dist/kg2bed.jar  [options] (stdin|file) 

Options

• -o|--output (OUTPUT-FILE) Output file. Default:stdout.
• -i|--intron Hide Introns Default value : "false".
• -u|--utr Hide UTRs Default value : "false".
• -c|--cds Hide CDSs Default value : "false".
• -x|--exon Hide Exons Default value : "false".
• -t|--transcript Hide Transcript Default value : "false".
• -h|--help print help
• -version|--version show version and exit

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/KnownGenesToBed.java

Example

$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz" |\
  gunzip -c |\
  java -jar dist/kg2bed.jar
chr1	11873	14409	+	uc001aaa.3	TRANSCRIPT	uc001aaa.3
chr1	11873	12227	+	uc001aaa.3	EXON	Exon 1
chr1	12227	12612	+	uc001aaa.3	INTRON	Intron 1
chr1	11873	12227	+	uc001aaa.3	UTR	UTR3
chr1	12612	12721	+	uc001aaa.3	EXON	Exon 2
chr1	12721	13220	+	uc001aaa.3	INTRON	Intron 2
chr1	12612	12721	+	uc001aaa.3	UTR	UTR3
chr1	13220	14409	+	uc001aaa.3	EXON	Exon 3
chr1	13220	14409	+	uc001aaa.3	UTR	UTR3
chr1	11873	14409	+	uc010nxr.1	TRANSCRIPT	uc010nxr.1
chr1	11873	12227	+	uc010nxr.1	EXON	Exon 1
chr1	12227	12645	+	uc010nxr.1	INTRON	Intron 1
chr1	11873	12227	+	uc010nxr.1	UTR	UTR3
chr1	12645	12697	+	uc010nxr.1	EXON	Exon 2
chr1	12697	13220	+	uc010nxr.1	INTRON	Intron 2

See also

• https://www.biostars.org/p/151628

History

• 2014: Creation
• 2015-07-21 : removed duplicate exon

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite kg2bed ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030