perl <-> java [was Re: [Bioperl-l] (no subject)]

Juguang Xiao juguang at
Wed Jun 18 18:13:18 EDT 2003

>> Hi, there,
>> I would like to know how to call bioperl method from
>> java. Any idea will be appreciated.

Do you want to pass objects or borrow functions from bioperl? This is 
too computer issue. A year ago, ensembl tried to solve the similar 
problem to top up ensembl-java usage and popularity, with no sounding 
result. I was working on it.

Actually we do not need to solve the problem on bioperl level.  
Methologically, you can pass the objects in file way, and compose a 
(perl/bash) script to assembly up the process written in bioperl and 
java. Or simple use bash's pipe

cmd1 | cmd2
Pipe; use output from cmd1 as input to cmd2.

Hope this tip help.
my  S$0.002

Juguang Xiao
Temasek Life Sciences Laboratory, National University of Singapore
1 Research Link,  Singapore 117604
juguang at

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