jvarkit

Biostar92368

Binary interactions depth.

Usage

Usage: biostar92368 [options] Files
  Options:
  * -D, --bdbhome
      berkeleydb home
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -M, --maxdepth
      Max depth
      Default: 3
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• protein
• interaction
• interactome

See also in Biostars

• https://www.biostars.org/p/92368

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 biostar92368

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/biostar/Biostar92368.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 biostar92368 ? 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

$ cat input.txt
A1	A2
A2	A3
A3	A4
A4	A5
A1	A6


$ mkdir -p tmp
$  java -jar dist/biostar92368.jar -D tmp input.txt

A1	A2	0
A1	A3	1
A1	A4	2
A1	A6	0
A2	A3	0
A2	A4	1
A2	A5	2
A2	A6	1
A3	A4	0
A3	A5	1
A3	A6	2
A4	A5	0

This site is open source. Improve this page.