UniprotFilterJS

Filters Uniprot DUMP+ XML with a javascript (java rhino) expression. Context contain 'entry' an uniprot entry and 'index', the index in the XML file.

Usage

Usage: java -jar dist/uniprotfilterjs.jar  [options] Files
Usage: uniprotfilterjs [options] Files
  Options:
    -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
    -e
       (js expression). Optional.
    -f
       (js file). Optional.

Keywords

• unitprot
• javascript
• xjc
• xml

Compilation

Requirements / Dependencies

• java compiler SDK 17. 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 --recurse-submodules "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew uniprotfilterjs

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/uniprot/UniprotFilterJS.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 uniprotfilterjs ? 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

the following script get the human (id=9606) uniprot entries having an id in ensembl:

function accept(e)
    {
    var ok=0,i;
    // check organism is human 
    if(e.getOrganism()==null) return false;
    var L= e.getOrganism().getDbReference();
    if(L==null) return false;
    for(i=0;i<L.size();++i)
        {
        if(L.get(i).getId()=="9606") {ok=1;break;}
        }
    if(ok==0) return false;
    ok=0;
    L= e.getDbReference();
    if(L==null) return false;
    for(i=0;i<L.size();++i)
        {
        if(L.get(i).getType()=="Ensembl") {ok=1;break;}
        }
    return ok==1;
    }
accept(entry);

$   curl -skL "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz" | gunzip -c |\
java -jar dist/uniprotfilterjs.jar  -f filter.js > output.xml