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

[Stephen Montgomery]

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 tll.org.sg
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
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).
Cheers,
Stephen