GenomicJaspar

##Motivation

Find jaspar ( http://jaspar.genereg.net/ ) patterns in FASTA sequences. Reports a BED file.

##Compilation

See also Compilation.

$  ant genomicjaspar

##Synopsis

$ java -jar dist/genomicjaspar.jar -J jaspar.pfm (stdin|file) 

##Options

Option	Description
-J (uri)	jaspar PFM uri/file. required. example: http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/pfm_vertebrates.txt
-f (0	raction of best score. default:0.95
-h	get help (this screen) and exit.
-v	print version and exit.
-L (level)	log level. One of java.util.logging.Level . Optional.

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/jaspar/GenomicJaspar.java ##Example

$ java -jar dist/genomicjaspar.jar  -J pfm_vertebrates.txt human_g1k_v37.fasta

1 dna:chromosome chromosome:GRCh37:1:1:249250621:1	10819	10825	MA0130.1 ZNF354C	978	-	6	ATCCAC	CTCCAC
1 dna:chromosome chromosome:GRCh37:1:1:249250621:1	10895	10901	MA0130.1 ZNF354C	978	-	6	ATCCAC	CTCCAC
1 dna:chromosome chromosome:GRCh37:1:1:249250621:1	10971	10977	MA0130.1 ZNF354C	978	-	6	ATCCAC	CTCCAC
1 dna:chromosome chromosome:GRCh37:1:1:249250621:1	11088	11094	MA0006.1 Arnt::Ahr	957	-	6	TGCGTG	CGCGTG
1 dna:chromosome chromosome:GRCh37:1:1:249250621:1	11104	11112	MA0067.1 Pax2	951	+	8	AGTCACGG	CGTCACGG
1 dna:chromosome chromosome:GRCh37:1:1:249250621:1	11421	11427	MA0056.1 MZF1_1-4	1000	+	6	TGGGGA	TGGGGA
1 dna:chromosome chromosome:GRCh37:1:1:249250621:1	11550	11558	MA0033.1 FOXL1	959	-	8	TATACATA	TAAACATA
1 dna:chromosome chromosome:GRCh37:1:1:249250621:1	11554	11560	MA0151.1 ARID3A	1000	-	6	ATTAAA	ATTAAA
1 dna:chromosome chromosome:GRCh37:1:1:249250621:1	11556	11561	MA0075.1 Prrx2	1000	-	5	AATTA	AATTA
1 dna:chromosome chromosome:GRCh37:1:1:249250621:1	11629	11635	MA0130.1 ZNF354C	978	+	6	ATCCAC	CTCCAC

##See also

• VcfJaspar
• http://www.biostars.org/p/90823/
• http://jaspar.genereg.net/

##History

• 2014: Creation