jvarkit

GexfTransformer

Gexf file manipulation

Usage

Usage: gexftr [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -c, --max-cluster
      limit to this number of clusters. Negative: no limit
      Default: 1
    -M, --max-nodes
      max number of nodes per cluster inclusive. Negative: no limit
      Default: -1
    -m, --min-nodes
      min number of nodes per cluster inclusive. Negative: no limit
      Default: -1
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• gexf
• graph
• network

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 gexftr

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/gephi/GexfTransformer.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 gexftr ? 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

Cluster

a Cluster is a set of nodes that are all connected with some edges.

Example:

$ java -jar dist/pubmeddump.jar "NSP1 Rotavirus" | \
  java -jar dist/pubmedauthorgraph.jar -D BDB |\
  java -jar dist/gexftr.jar | xmllint --format - 
  
(...)
      <!--Skip edge  from HOWARD~C_R to pmid:9614866-->
      <!--Skip edge  from BRIDGER~J_C to pmid:9614866-->
      <!--Skip edge  from LÓPEZ~S to pmid:9645203-->
      <!--Skip edge  from GONZÁLEZ~R_A to pmid:9645203-->
      <!--Skip edge  from ARIAS~C_F to pmid:9645203-->
      <!--Skip edge  from TORRES-VEGA~M_A to pmid:9645203-->
    </edges>
  </graph>
  <!--Number of nodes 692-->
</gexf>

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