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

Stephen Montgomery smontgom at
Wed Jun 18 11:23:08 EDT 2003

Juguang Xiao wrote:

>>> 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
>  ------------ATGCCGAGCTTNNNNCT--------------
> Juguang Xiao
> Temasek Life Sciences Laboratory, National University of Singapore
> 1 Research Link,  Singapore 117604
> juguang at
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at
You could alternatively use something like Java webservices which would 
use SOAP to pass objects - this is designed to be language independent 
but the details of which version of SOAP to use are still unclear (an 
IBM / Microsoft thing - I hear).

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