Gff2KnownGene

##Motivation

Convert GFF3 format to UCSC knownGene format.

##Compilation

Requirements / Dependencies

java 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
apache ant is only required to compile htsjdk
xsltproc http://xmlsoft.org/XSLT/xsltproc2.html

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make gff2kg

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 addinging standalone=yes on the command line:

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make gff2kg 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 paths.

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/gff2kg.jar  [options] (stdin|file)

Options

-o|--output (OUTPUT-FILE) Output file. Default:stdout
-maxRecordsInRam|--maxRecordsInRam (NUMBER) When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort a SAM/VCF/... file, and increases the amount of RAM needed. Default value : "500000".
-tmpdir|--tmpdir (TMPDIR) Set temporary directory
-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/Gff2KnownGene.java



### Example
$  curl -s "ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gff3.gz" | gunzip -c | java -jar dist/gff2kg.jar
(...)
1826	ENST00000367917.3	chr1	+	162760522	162782607	162760590	162782210	8	162760522,162762448,162766374,162767591,162769532,162774056,162775183,162782087	162760625,162762652,162766467,162767706,162769727,162774113,162775282,162782607	gene_id=ENSG00000132196.9;transcript_id=ENST00000367917.3;gene_type=protein_coding;gene_status=KNOWN;gene_name=HSD17B7;transcript_type=protein_coding;transcript_name=HSD17B7-201;protein_id=ENSP00000356894.3;havana_gene=OTTHUMG00000034420.6;	ENST00000367917.3
(...)

In the UCSC (not the structure of konwGene, but we can validate intervals):


$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -D hg19 -e 'select * from wgEncodeGencodeBasicV19 where name="ENST00000367917.3"' | cat
bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
1826	ENST00000367917.3	chr1	+	162760522	162782607	162760590	162782210	8	162760522,162762448,162766374,162767591,162769532,162774056,162775183,162782087,	162760625,162762652,162766467,162767706,162769727,162774113,162775282,162782607,	0	HSD17B7	cmpl	cmpl	0,2,2,2,0,0,0,0,