jvarkit

Gff2KnownGene

Last commit

Convert GFF3 format to UCSC knownGene format.

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar gff2kg  [options] Files

Usage: gff2kg [options] Files
  Options:
    -bed12, --bed12
      Ouput bed.
      Default: false
    -bin, --bin
      Insert  UCSC 'bin' column as the first column.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

gff
,gtf
knownGene
ucsc
convert

Creation Date

20160404

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/gff2kg/Gff2KnownGene.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/gff2kg/Gff2KnownGeneTest.java

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 gff2kg ? 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

Example

$  curl -s "ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gff3.gz" |\
	gunzip -c |\
	java -jar dist/jvarkit.jar gff2kg
(...)
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,

From ensembl

$	wget -O -  "ftp://ftp.ensembl.org/pub/grch37/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh37.82.gtf.gz" |\
	gunzip -c |\
	java -jar dist/jvarkit.jar gff2kg