MapUniProtFeatures

##Motivation map uniprot features on reference genome.

##Options

Option	Description
-R File	Fasta Genome Reference Required.
-o File	output name (default: stdout) Required.
-k String	KnownGene data Default value: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz. This option can be set to 'null' to clear the default value.
-u String	Uniprot URL/File Default value: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz. This option can be set to 'null' to clear the default value.

##Source Code

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

##Example

$ java  -jar dist/mapuniprot.jar \
	-R /path/to/human_g1k_v37.fasta \
	-u /path/uri/uniprot.org/uniprot_sprot.xml.gz  \
	-k <(curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz" | gunzip -c | awk -F '        ' '{if($2 ~ ".*_.*") next; OFS="       "; gsub(/chr/,"",$2);print;}'   ) |\
	LC_ALL=C sort -t '	' -k1,1 -k2,2n -k3,3n  | uniq | head


1	69090	69144	topological_domain	1000	+	69090	69144	255,0,0	1	54	0
1	69144	69216	transmembrane_region	1000	+	69144	69216	255,0,0	1	72	0
1	69216	69240	topological_domain	1000	+	69216	69240	255,0,0	1	24	0
1	69240	69306	transmembrane_region	1000	+	69240	69306	255,0,0	1	66	0
1	69306	69369	topological_domain	1000	+	69306	69369	255,0,0	1	63	0
1	69357	69636	disulfide_bond	1000	+	69357	69636	255,0,0	1	279	0
1	69369	69429	transmembrane_region	1000	+	69369	69429	255,0,0	1	60	0
1	69429	69486	topological_domain	1000	+	69429	69486	255,0,0	1	57	0
1	69486	69543	transmembrane_region	1000	+	69486	69543	255,0,0	1	57	0
1	69543	69654	topological_domain	1000	+	69543	69654	255,0,0	1	111	0

Contribute

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

##See also

##History

• 2013 : Creation

License

The project is licensed under the MIT license.