Biostar92368

##Motivation Number of intermediate interactors between proteins: http://www.biostars.org/p/92368/

##Compilation

Requires berkeley DB java edition : http://www.oracle.com/technetwork/database/berkeleydb/overview/index-093405.html

See also Compilation.

set the path of berkeleydb je in 'build.properties'

berkeleydb.jar=/path/to/je-4.1.10/lib/je-4.1.10.jar
picard.version=1.100
picard.dir=/path/to/picard-tools-${picard.version}

$ make biostar92368

##Synopsis

$ java -jar dist/biostar92368.jar -D dir (stdin|files) 

##Options

Option	Description
-D (dir)	berkeleydb home. REQUIRED.
-M (max depth)	default:3
-h	get help (this screen) and exit.
-v	print version and exit.
-L (level)	log level. One of java.util.logging.Level . Optional.

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar92368.java

##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

##See also

• http://www.biostars.org/p/92368/

##History

• 2014: Creation