map uniprot features on reference genome
Usage: java -jar dist/mapuniprot.jar [options] Files
Usage: mapuniprot [options] Files
Options:
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
--version
print version and exit
-R
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard CreateSequenceDictionary
-k
UCSC knownGene File/URL. The knowGene format is a compact alternative to
GFF/GTF because one transcript is described using only one line. Beware
chromosome names are formatted the same as your REFERENCE. A typical
KnownGene file is
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz
.If you only have a gff file, you can try to generate a knownGene file
with [http://lindenb.github.io/jvarkit/Gff2KnownGene.html](http://lindenb.github.io/jvarkit/Gff2KnownGene.html)
Default: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz
-o
Output file. Optional . Default: stdout
-u
Uniprot.xml.gz URL/File.
Default: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew mapuniprot
The java jar file will be installed in the dist
directory.
The project is licensed under the MIT license.
Should you cite mapuniprot ? 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
$ 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