jvarkit

MapUniProtFeatures

map uniprot features on reference genome

Usage

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

Keywords

• uniprot
• bed
• fasta
• reference
• xjc
• xml

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew mapuniprot

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/MapUniProtFeatures.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 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

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